PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:19.036
Source: plumed.dat
Originally used with PLUMED version: 2.2
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=9,20,37,53,67,77,96,110,129,146,156,175,196,207,226,242,253,269,285,292,311,331,338,352,372,391,407,424,445,461,480,496,520,541,555,577,594,616,630,640,654,668,687,708,727,747,761,780,790,809,819,831,841,860,870,884,895,909,930,942,962,979,990,1006,1020,1041,1060,1077,1084,1098,1124,1136,1156,1163,1177,1196,1215,1225,1247,1266,1282,1301,1312,1331,1343,1364,1385,1399,1416,1436,1450,1461,1480,1500,1514,1533,1544,1558,1575,1586,1602,1614,1638,1659,1678,1688,1704,1715,1734,1746,1762,1784,1794,1813,1825,1845,1869,1885,1897,1921,1935,1945,1967,1986,2002,2016,2032,2043,2057,2081,2100,2119,2130,2141,2151,2170,2177,2198,2210,2226,2243,2263,2280,2290,2304,2318,2340,2361,2385,2402,2409,2420,2439,2451,2461,2475,2494,2508,2528,2539,2558,2570,2584,2608,2629,2653,2668,2682,2701,2720,2742,2761,2772,2788,2808,2827,2847,2857,2877,2896,2915,2927,2943,2962,2981,3000,3014,3030,3041,3062,3069,3088,3105,3124,3143,3167,3186,3208,3219,3235,3259,3276,3295,3306,3313,3324,3346,3361,3383,3395,3419,3433,3452,3476,3500,3519,3533,3557,3574,3590,3609,3625,3641,3657,3667,3683,3703,3722,3738,3749,3773,3789,3801,3820,3837,3856,3877,3893,3912,3931,3953,3963,3982,4001,4015,4036,4048,4063,4077,4091,4111,4128,4142,4158,4169,4193,4210,4230,4241,4260,4270,4289,4296,4317,4331,4345,4356,4367,4386,4402,4414,4430,4449,4470,4480,4500,4519,4531,4546,4560,4580,4602,4626,4637,4657,4681,4696,4716,4727

# define sidechain center of mass
The WHOLEMOLECULES action with label  calculates somethingcom275The COM action with label com275 calculates the following quantities: Quantity    Type    Description  
com275 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3435,3438,3440,3444
com278The COM action with label com278 calculates the following quantities: Quantity    Type    Description  
com278 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3502,3504,3508,3511
com279The COM action with label com279 calculates the following quantities: Quantity    Type    Description  
com279 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3521,3523,3525
com282The COM action with label com282 calculates the following quantities: Quantity    Type    Description  
com282 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3576,3578,3582
com283The COM action with label com283 calculates the following quantities: Quantity    Type    Description  
com283 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3592,3595,3597,3601
com286The COM action with label com286 calculates the following quantities: Quantity    Type    Description  
com286 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3643,3645,3649
com336The COM action with label com336 calculates the following quantities: Quantity    Type    Description  
com336 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4451,4454,4455,4457,4459,4460,4462,4464
com337The COM action with label com337 calculates the following quantities: Quantity    Type    Description  
com337 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4472
com338The COM action with label com338 calculates the following quantities: Quantity    Type    Description  
com338 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4482,4485,4486,4488,4490,4492,4494
com340The COM action with label com340 calculates the following quantities: Quantity    Type    Description  
com340 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4521,4524,4525,4526
com342The COM action with label com342 calculates the following quantities: Quantity    Type    Description  
com342 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4548,4551,4552,4553
com343The COM action with label com343 calculates the following quantities: Quantity    Type    Description  
com343 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4562,4565,4566,4568,4570,4572,4574
com346The COM action with label com346 calculates the following quantities: Quantity    Type    Description  
com346 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4628,4631
com168The COM action with label com168 calculates the following quantities: Quantity    Type    Description  
com168 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1680
com103The COM action with label com103 calculates the following quantities: Quantity    Type    Description  
com103 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=642,644,646
com259The COM action with label com259 calculates the following quantities: Quantity    Type    Description  
com259 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3169,3172,3174,3178
com165The COM action with label com165 calculates the following quantities: Quantity    Type    Description  
com165 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1616,1619,1622,1625,1627,1628,1631
com256The COM action with label com256 calculates the following quantities: Quantity    Type    Description  
com256 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3107,3109,3113,3116
com161The COM action with label com161 calculates the following quantities: Quantity    Type    Description  
com161 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1560,1563,1566,1567
com252The COM action with label com252 calculates the following quantities: Quantity    Type    Description  
com252 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3043,3046,3047,3049,3051,3052,3054,3056
com158The COM action with label com158 calculates the following quantities: Quantity    Type    Description  
com158 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1516,1519,1521,1525
com89The COM action with label com89 calculates the following quantities: Quantity    Type    Description  
com89 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=393,395,399
com107The COM action with label com107 calculates the following quantities: Quantity    Type    Description  
com107 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=710,712,716,719
com88The COM action with label com88 calculates the following quantities: Quantity    Type    Description  
com88 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=374,377,379,383
com281The COM action with label com281 calculates the following quantities: Quantity    Type    Description  
com281 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3559,3562,3565,3566
com98The COM action with label com98 calculates the following quantities: Quantity    Type    Description  
com98 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=557,560,563,566,569
com99The COM action with label com99 calculates the following quantities: Quantity    Type    Description  
com99 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=579,582,585,586
com97The COM action with label com97 calculates the following quantities: Quantity    Type    Description  
com97 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=543,545,547

## define contact maps 
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.249857 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.061711 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.09418 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.913337 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.103865 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.807876 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.266732 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.192009 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.156299 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.670815 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.980946 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.868537 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.672935 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.819709 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.066932 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.049462 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.933018 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.249603 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.143456 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.091051 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.056638 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.915274 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.908882 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.02255 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.860216 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.255458 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.246709 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.948101 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c1The CONTACTMAP action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.038146 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.034676 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.057035 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.787934 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.0599 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.799266 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.106634 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.182876 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.142227 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.803214 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.956525 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.804572 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.039985 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.115525 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.091841 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.126271 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.899862 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.510023 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.056161 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.093013 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.050191 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.365286 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.940251 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.013979 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.954454 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.322778 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.245941 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.861337 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c2The CONTACTMAP action with label c2 calculates the following quantities: Quantity    Type    Description  
c2 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.184308 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.169323 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.147947 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.780345 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.15826 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.580143 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.243738 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.138726 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.24089 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.482493 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.653199 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.303673 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.029317 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.051622 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.361263 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.053851 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.923406 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.442498 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.181963 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.07063 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.03647 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.939419 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.948476 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.027995 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.934265 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.356744 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.395709 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.437787 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c3The CONTACTMAP action with label c3 calculates the following quantities: Quantity    Type    Description  
c3 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.236583 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.148989 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.201936 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.671497 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.278128 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.237123 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.418129 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.752275 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.655172 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.112907 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.38151 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.081027 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.056547 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.059857 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.870658 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.119351 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.881695 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.149385 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.122076 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.025532 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.038864 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.952423 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.892655 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.044675 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.940302 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.33593 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.341799 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.466959 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c4The CONTACTMAP action with label c4 calculates the following quantities: Quantity    Type    Description  
c4 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.048216 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.037817 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.087432 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.863689 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.223027 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.307027 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.643698 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.725015 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.801528 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.152721 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.463099 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.105594 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.11966 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.121688 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.573213 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.091447 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.853899 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.250448 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.096787 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.049064 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.078775 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.142918 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.902978 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.022543 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.609483 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.758811 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.682149 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.486591 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c5The CONTACTMAP action with label c5 calculates the following quantities: Quantity    Type    Description  
c5 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.387548 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.202362 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.644502 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.531403 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.733564 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.119282 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.874487 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.902964 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.787433 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.099733 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.586716 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.121648 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.113451 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.129908 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.943281 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.10848 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.865847 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.147303 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.099715 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.217403 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.066791 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.224049 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.902805 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.159987 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.492634 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.863426 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.879098 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.476811 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c6The CONTACTMAP action with label c6 calculates the following quantities: Quantity    Type    Description  
c6 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.310848 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.089484 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.890419 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.331245 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.753251 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.098724 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.878114 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.888719 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.85734 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.1665 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.484685 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.133632 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.090849 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.114134 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.832883 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.461945 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.322961 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.096265 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.678814 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.053257 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.054849 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.100987 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.267064 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.382232 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.445273 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.719075 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.868918 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.487404 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c7The CONTACTMAP action with label c7 calculates the following quantities: Quantity    Type    Description  
c7 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.665278 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.42436 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.630523 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.284663 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.819502 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.097611 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.916252 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.785366 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.768668 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.202085 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.381252 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.135745 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.083387 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.090894 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.780244 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.555834 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.221895 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.112654 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.555089 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.949592 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.067074 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.043662 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.322581 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.238716 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.464645 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.724434 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.652893 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.408324 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c8The CONTACTMAP action with label c8 calculates the following quantities: Quantity    Type    Description  
c8 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.46124 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.710498 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.951161 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.200454 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.870356 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.047865 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.876758 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.869338 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.63314 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.105683 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.47159 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.075247 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.061127 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.09285 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.795682 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.396952 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.309016 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.066342 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.474607 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.761112 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.059645 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.09394 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.917295 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.93787 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.178024 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.543894 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.699641 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.443878 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c9The CONTACTMAP action with label c9 calculates the following quantities: Quantity    Type    Description  
c9 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.286972 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.8136 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.946058 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.102016 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.924682 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.031102 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.837152 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.912847 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.679904 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.109588 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.255692 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.044485 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.033564 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.049912 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.932087 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.558561 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.228515 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.240334 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.884638 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.817287 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.059845 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.044122 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.236806 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.952191 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.576779 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.835276 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.794769 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.371188 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=c10The CONTACTMAP action with label c10 calculates the following quantities: Quantity    Type    Description  
c10 scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.79593 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.91331 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.89347 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.10945 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.93014 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.03243 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.85785 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.8836 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.82381 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.14567 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.22559 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.10374 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.04386 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.04773 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.88323 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.68472 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.24331 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.21303 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.83723 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.70598 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.92732 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.01748 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.10352 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.79672 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.16134 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.8049 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.83919 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.23727 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=cmapinaTMThe CONTACTMAP action with label cmapinaTM calculates the following quantities: Quantity    Type    Description  
cmapinaTM scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP


CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=com168,com275 REFERENCE1A reference value for a given contact, by default is 0=0.03953 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=com103,com278 REFERENCE2A reference value for a given contact, by default is 0=0.03714 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=com165,com279 REFERENCE3A reference value for a given contact, by default is 0=0.05943 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=com256,com279 REFERENCE4A reference value for a given contact, by default is 0=0.91797 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS5the atoms involved in each of the contacts you wish to calculate=com161,com282 REFERENCE5A reference value for a given contact, by default is 0=0.06853 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS6the atoms involved in each of the contacts you wish to calculate=com256,com282 REFERENCE6A reference value for a given contact, by default is 0=0.82084 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS7the atoms involved in each of the contacts you wish to calculate=com252,com283 REFERENCE7A reference value for a given contact, by default is 0=0.16191 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS8the atoms involved in each of the contacts you wish to calculate=com158,com286 REFERENCE8A reference value for a given contact, by default is 0=0.18377 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS9the atoms involved in each of the contacts you wish to calculate=com89,com336 REFERENCE9A reference value for a given contact, by default is 0=0.12424 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS10the atoms involved in each of the contacts you wish to calculate=com158,com336 REFERENCE10A reference value for a given contact, by default is 0=0.81203 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS11the atoms involved in each of the contacts you wish to calculate=com89,com337 REFERENCE11A reference value for a given contact, by default is 0=0.95699 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS12the atoms involved in each of the contacts you wish to calculate=com107,com337 REFERENCE12A reference value for a given contact, by default is 0=0.91304 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS13the atoms involved in each of the contacts you wish to calculate=com88,com338 REFERENCE13A reference value for a given contact, by default is 0=0.7162 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS14the atoms involved in each of the contacts you wish to calculate=com89,com338 REFERENCE14A reference value for a given contact, by default is 0=0.74479 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS15the atoms involved in each of the contacts you wish to calculate=com281,com340 REFERENCE15A reference value for a given contact, by default is 0=0.15873 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.65 MM=10}
ATOMS16the atoms involved in each of the contacts you wish to calculate=826,1392 REFERENCE16A reference value for a given contact, by default is 0=0.01999 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS17the atoms involved in each of the contacts you wish to calculate=1328,1392 REFERENCE17A reference value for a given contact, by default is 0=0.91467 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS18the atoms involved in each of the contacts you wish to calculate=825,1455 REFERENCE18A reference value for a given contact, by default is 0=0.91655 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS19the atoms involved in each of the contacts you wish to calculate=1392,1455 REFERENCE19A reference value for a given contact, by default is 0=0.03419 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS20the atoms involved in each of the contacts you wish to calculate=644,1628 REFERENCE20A reference value for a given contact, by default is 0=0.03693 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS21the atoms involved in each of the contacts you wish to calculate=753,2065 REFERENCE21A reference value for a given contact, by default is 0=0.05593 SWITCH21The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS22the atoms involved in each of the contacts you wish to calculate=1628,3052 REFERENCE22A reference value for a given contact, by default is 0=0.91104 SWITCH22The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS23the atoms involved in each of the contacts you wish to calculate=3380,3431 REFERENCE23A reference value for a given contact, by default is 0=0.85941 SWITCH23The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS24the atoms involved in each of the contacts you wish to calculate=1625,3523 REFERENCE24A reference value for a given contact, by default is 0=0.00813 SWITCH24The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS25the atoms involved in each of the contacts you wish to calculate=186,4198 REFERENCE25A reference value for a given contact, by default is 0=0.90375 SWITCH25The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS26the atoms involved in each of the contacts you wish to calculate=1031,4198 REFERENCE26A reference value for a given contact, by default is 0=0.10755 SWITCH26The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS27the atoms involved in each of the contacts you wish to calculate=4393,4460 REFERENCE27A reference value for a given contact, by default is 0=0.13625 SWITCH27The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
ATOMS28the atoms involved in each of the contacts you wish to calculate=4411,4478 REFERENCE28A reference value for a given contact, by default is 0=0.88731 SWITCH28The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.45 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=cmapacTMThe CONTACTMAP action with label cmapacTM calculates the following quantities: Quantity    Type    Description  
cmapacTM scalar the sum of all the switching function on all the distances
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

# RMSDs
rmsd1The RMSD action with label rmsd1 calculates the following quantities: Quantity    Type    Description  
rmsd1 scalar the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=ref_active.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd1: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=ref_active.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
rmsd2The RMSD action with label rmsd2 calculates the following quantities: Quantity    Type    Description  
rmsd2 scalar the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=ref_inactive.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd2: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=ref_inactive.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

# TM6-TM3 dists:
comtm3The COM action with label comtm3 calculates the following quantities: Quantity    Type    Description  
comtm3 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1614,1638,1659,1678,1688,1704
comtm6The COM action with label comtm6 calculates the following quantities: Quantity    Type    Description  
comtm6 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3395,3419,3433,3452,3476,3500
distThe DISTANCE action with label dist calculates the following quantities: Quantity    Type    Description  
dist scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=comtm3,comtm6

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd1,rmsd2,dist,cmapinaTM,cmapacTM STRIDE the frequency with which the quantities of interest should be output=625 FILEthe name of the file on which to output these quantities=RMSD

# The contact map references
p1The FUNCPATHMSD action with label p1 calculates the following quantities: Quantity    Type    Description  
p1.s scalar the position on the path
p1.z scalar the distance from the path: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=c1,c2,c3,c4,c5,c6,c7,c8,c9,c10 LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=2.020093
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,p1.s,p1.z STRIDE the frequency with which the quantities of interest should be output=625 FILEthe name of the file on which to output these quantities=colvar1

# Metadynamics
metaThe METAD action with label meta calculates the following quantities: Quantity    Type    Description  
meta.bias scalar the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=p1.s,p1.z PACEthe frequency for hill addition=1250 SIGMAthe widths of the Gaussian hills=0.1,0.05 HEIGHTthe heights of the Gaussian hills=1.6 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=12 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0.0,-1.0 GRID_MAXthe upper bounds for the grid=10.0,6.0
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p1.s,p1.z,meta.* STRIDE the frequency with which the quantities of interest should be output=625 FILEthe name of the file on which to output these quantities=colvar2

ENDPLUMEDTerminate plumed input. More details
Quantity	Type	Description
com275	atoms	virtual atom calculated by COM action
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
