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
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WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=9,20,37,53,67,77,96,110,129,146,156,175,196,207,226,242,253,269,285,292,311,331,338,352,372,391,407,424,445,461,480,496,520,541,555,577,594,616,630,640,654,668,687,708,727,747,761,780,790,809,819,831,841,860,870,884,895,909,930,942,962,979,990,1006,1020,1041,1060,1077,1084,1098,1124,1136,1156,1163,1177,1196,1215,1225,1247,1266,1282,1301,1312,1331,1343,1364,1385,1399,1416,1436,1450,1461,1480,1500,1514,1533,1544,1558,1575,1586,1602,1614,1638,1659,1678,1688,1704,1715,1734,1746,1762,1784,1794,1813,1825,1845,1869,1885,1897,1921,1935,1945,1967,1986,2002,2016,2032,2043,2057,2081,2100,2119,2130,2141,2151,2170,2177,2198,2210,2226,2243,2263,2280,2290,2304,2318,2340,2361,2385,2402,2409,2420,2439,2451,2461,2475,2494,2508,2528,2539,2558,2570,2584,2608,2629,2653,2668,2682,2701,2720,2742,2761,2772,2788,2808,2827,2847,2857,2877,2896,2915,2927,2943,2962,2981,3000,3014,3030,3041,3062,3069,3088,3105,3124,3143,3167,3186,3208,3219,3235,3259,3276,3295,3306,3313,3324,3346,3361,3383,3395,3419,3433,3452,3476,3500,3519,3533,3557,3574,3590,3609,3625,3641,3657,3667,3683,3703,3722,3738,3749,3773,3789,3801,3820,3837,3856,3877,3893,3912,3931,3953,3963,3982,4001,4015,4036,4048,4063,4077,4091,4111,4128,4142,4158,4169,4193,4210,4230,4241,4260,4270,4289,4296,4317,4331,4345,4356,4367,4386,4402,4414,4430,4449,4470,4480,4500,4519,4531,4546,4560,4580,4602,4626,4637,4657,4681,4696,4716,4727the atoms that make up a molecule that you wish to align
# define sidechain center of mass com275:COMCalculate the center of mass for a group of atoms. More detailsATOMS=3435,3438,3440,3444 com278:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3502,3504,3508,3511 com279:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3521,3523,3525 com282:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3576,3578,3582 com283:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3592,3595,3597,3601 com286:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3643,3645,3649 com336:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4451,4454,4455,4457,4459,4460,4462,4464 com337:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4472 com338:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4482,4485,4486,4488,4490,4492,4494 com340:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4521,4524,4525,4526 com342:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4548,4551,4552,4553 com343:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4562,4565,4566,4568,4570,4572,4574 com346:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=4628,4631 com168:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1680 com103:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=642,644,646 com259:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3169,3172,3174,3178 com165:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1616,1619,1622,1625,1627,1628,1631 com256:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3107,3109,3113,3116 com161:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1560,1563,1566,1567 com252:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3043,3046,3047,3049,3051,3052,3054,3056 com158:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1516,1519,1521,1525 com89:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=393,395,399 com107:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=710,712,716,719 com88:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=374,377,379,383 com281:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3559,3562,3565,3566 com98:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=557,560,563,566,569 com99:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=579,582,585,586 com97:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=543,545,547the list of atoms which are involved the virtual atom's definition
## define contact mapsCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.249857A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.061711A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.09418A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.913337A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.103865A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.807876A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.266732A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.192009A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.156299A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.670815A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.980946A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.868537A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.672935A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.819709A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.066932A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.049462A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.933018A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.249603A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.143456A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.091051A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.056638A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.915274A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.908882A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.02255A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.860216A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.255458A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.246709A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.948101A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c1a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.038146A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.034676A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.057035A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.787934A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.0599A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.799266A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.106634A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.182876A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.142227A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.803214A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.956525A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.804572A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.039985A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.115525A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.091841A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.126271A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.899862A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.510023A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.056161A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.093013A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.050191A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.365286A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.940251A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.013979A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.954454A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.322778A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.245941A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.861337A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c2a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.184308A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.169323A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.147947A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.780345A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.15826A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.580143A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.243738A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.138726A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.24089A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.482493A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.653199A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.303673A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.029317A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.051622A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.361263A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.053851A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.923406A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.442498A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.181963A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.07063A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.03647A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.939419A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.948476A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.027995A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.934265A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.356744A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.395709A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.437787A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c3a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.236583A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.148989A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.201936A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.671497A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.278128A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.237123A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.418129A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.752275A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.655172A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.112907A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.38151A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.081027A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.056547A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.059857A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.870658A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.119351A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.881695A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.149385A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.122076A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.025532A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.038864A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.952423A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.892655A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.044675A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.940302A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.33593A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.341799A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.466959A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c4a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.048216A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.037817A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.087432A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.863689A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.223027A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.307027A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.643698A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.725015A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.801528A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.152721A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.463099A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.105594A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.11966A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.121688A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.573213A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.091447A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.853899A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.250448A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.096787A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.049064A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.078775A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.142918A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.902978A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.022543A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.609483A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.758811A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.682149A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.486591A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c5a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.387548A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.202362A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.644502A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.531403A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.733564A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.119282A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.874487A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.902964A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.787433A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.099733A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.586716A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.121648A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.113451A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.129908A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.943281A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.10848A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.865847A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.147303A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.099715A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.217403A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.066791A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.224049A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.902805A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.159987A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.492634A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.863426A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.879098A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.476811A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c6a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.310848A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.089484A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.890419A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.331245A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.753251A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.098724A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.878114A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.888719A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.85734A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.1665A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.484685A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.133632A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.090849A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.114134A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.832883A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.461945A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.322961A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.096265A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.678814A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.053257A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.054849A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.100987A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.267064A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.382232A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.445273A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.719075A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.868918A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.487404A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c7a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.665278A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.42436A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.630523A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.284663A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.819502A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.097611A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.916252A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.785366A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.768668A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.202085A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.381252A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.135745A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.083387A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.090894A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.780244A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.555834A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.221895A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.112654A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.555089A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.949592A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.067074A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.043662A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.322581A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.238716A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.464645A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.724434A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.652893A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.408324A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c8a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.46124A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.710498A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.951161A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.200454A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.870356A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.047865A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.876758A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.869338A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.63314A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.105683A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.47159A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.075247A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.061127A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.09285A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.795682A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.396952A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.309016A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.066342A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.474607A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.761112A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.059645A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.09394A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.917295A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.93787A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.178024A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.543894A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.699641A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.443878A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c9a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.286972A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.8136A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.946058A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.102016A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.924682A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.031102A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.837152A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.912847A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.679904A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.109588A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.255692A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.044485A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.033564A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.049912A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.932087A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.558561A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.228515A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.240334A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.884638A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.817287A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.059845A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.044122A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.236806A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.952191A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.576779A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.835276A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.794769A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.371188A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=c10a label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.79593A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.91331A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.89347A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.10945A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.93014A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.03243A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.85785A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.8836A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.82381A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.14567A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.22559A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.10374A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.04386A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.04773A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.88323A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.68472A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.24331A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.21303A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.83723A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.70598A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.92732A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.01748A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.10352A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.79672A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.16134A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.8049A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.83919A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.23727A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=cmapinaTMa label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact mapCONTACTMAP...Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=com168,com275the atoms involved in each of the contacts you wish to calculateREFERENCE1=0.03953A reference value for a given contact, by default is 0SWITCH1={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS2=com103,com278the atoms involved in each of the contacts you wish to calculateREFERENCE2=0.03714A reference value for a given contact, by default is 0SWITCH2={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS3=com165,com279the atoms involved in each of the contacts you wish to calculateREFERENCE3=0.05943A reference value for a given contact, by default is 0SWITCH3={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS4=com256,com279the atoms involved in each of the contacts you wish to calculateREFERENCE4=0.91797A reference value for a given contact, by default is 0SWITCH4={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS5=com161,com282the atoms involved in each of the contacts you wish to calculateREFERENCE5=0.06853A reference value for a given contact, by default is 0SWITCH5={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS6=com256,com282the atoms involved in each of the contacts you wish to calculateREFERENCE6=0.82084A reference value for a given contact, by default is 0SWITCH6={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS7=com252,com283the atoms involved in each of the contacts you wish to calculateREFERENCE7=0.16191A reference value for a given contact, by default is 0SWITCH7={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS8=com158,com286the atoms involved in each of the contacts you wish to calculateREFERENCE8=0.18377A reference value for a given contact, by default is 0SWITCH8={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS9=com89,com336the atoms involved in each of the contacts you wish to calculateREFERENCE9=0.12424A reference value for a given contact, by default is 0SWITCH9={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS10=com158,com336the atoms involved in each of the contacts you wish to calculateREFERENCE10=0.81203A reference value for a given contact, by default is 0SWITCH10={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS11=com89,com337the atoms involved in each of the contacts you wish to calculateREFERENCE11=0.95699A reference value for a given contact, by default is 0SWITCH11={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS12=com107,com337the atoms involved in each of the contacts you wish to calculateREFERENCE12=0.91304A reference value for a given contact, by default is 0SWITCH12={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS13=com88,com338the atoms involved in each of the contacts you wish to calculateREFERENCE13=0.7162A reference value for a given contact, by default is 0SWITCH13={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS14=com89,com338the atoms involved in each of the contacts you wish to calculateREFERENCE14=0.74479A reference value for a given contact, by default is 0SWITCH14={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS15=com281,com340the atoms involved in each of the contacts you wish to calculateREFERENCE15=0.15873A reference value for a given contact, by default is 0SWITCH15={RATIONAL R_0=0.65 MM=10}The switching functions to use for each of the contacts in your mapATOMS16=826,1392the atoms involved in each of the contacts you wish to calculateREFERENCE16=0.01999A reference value for a given contact, by default is 0SWITCH16={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS17=1328,1392the atoms involved in each of the contacts you wish to calculateREFERENCE17=0.91467A reference value for a given contact, by default is 0SWITCH17={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS18=825,1455the atoms involved in each of the contacts you wish to calculateREFERENCE18=0.91655A reference value for a given contact, by default is 0SWITCH18={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS19=1392,1455the atoms involved in each of the contacts you wish to calculateREFERENCE19=0.03419A reference value for a given contact, by default is 0SWITCH19={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS20=644,1628the atoms involved in each of the contacts you wish to calculateREFERENCE20=0.03693A reference value for a given contact, by default is 0SWITCH20={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS21=753,2065the atoms involved in each of the contacts you wish to calculateREFERENCE21=0.05593A reference value for a given contact, by default is 0SWITCH21={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS22=1628,3052the atoms involved in each of the contacts you wish to calculateREFERENCE22=0.91104A reference value for a given contact, by default is 0SWITCH22={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS23=3380,3431the atoms involved in each of the contacts you wish to calculateREFERENCE23=0.85941A reference value for a given contact, by default is 0SWITCH23={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS24=1625,3523the atoms involved in each of the contacts you wish to calculateREFERENCE24=0.00813A reference value for a given contact, by default is 0SWITCH24={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS25=186,4198the atoms involved in each of the contacts you wish to calculateREFERENCE25=0.90375A reference value for a given contact, by default is 0SWITCH25={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS26=1031,4198the atoms involved in each of the contacts you wish to calculateREFERENCE26=0.10755A reference value for a given contact, by default is 0SWITCH26={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS27=4393,4460the atoms involved in each of the contacts you wish to calculateREFERENCE27=0.13625A reference value for a given contact, by default is 0SWITCH27={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapATOMS28=4411,4478the atoms involved in each of the contacts you wish to calculateREFERENCE28=0.88731A reference value for a given contact, by default is 0SWITCH28={RATIONAL R_0=0.45 MM=10}The switching functions to use for each of the contacts in your mapLABEL=cmapacTMa label for the action so that its output can be referenced in the input to other actionsCMDIST... CONTACTMAPcalculate the distance with respect to the provided reference contact map
# RMSDs rmsd1:RMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=ref_active.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd2:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=ref_inactive.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performed
# TM6-TM3 dists: comtm3:COMCalculate the center of mass for a group of atoms. More detailsATOMS=1614,1638,1659,1678,1688,1704 comtm6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3395,3419,3433,3452,3476,3500 dist:the list of atoms which are involved the virtual atom's definitionDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=comtm3,comtm6the pair of atom that we are calculating the distance betweenPrint quantities to a file. More detailsARG=rmsd1,rmsd2,dist,cmapinaTM,cmapacTMthe input for this action is the scalar output from one or more other actionsSTRIDE=625the frequency with which the quantities of interest should be outputFILE=RMSDthe name of the file on which to output these quantities
# The contact map references p1:FUNCPATHMSDThis function calculates path collective variables. More detailsARG=c1,c2,c3,c4,c5,c6,c7,c8,c9,c10the input for this action is the scalar output from one or more other actionsLAMBDA=2.020093the lambda parameter is needed for smoothing, is in the units of plumedPrint quantities to a file. More detailsARG=c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,p1.s,p1.zthe input for this action is the scalar output from one or more other actionsSTRIDE=625the frequency with which the quantities of interest should be outputFILE=colvar1the name of the file on which to output these quantities
# Metadynamics meta:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=p1.s,p1.zthe input for this action is the scalar output from one or more other actionsPACE=1250the frequency for hill additionSIGMA=0.1,0.05the widths of the Gaussian hillsHEIGHT=1.6the heights of the Gaussian hillsTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=12use well tempered metadynamics and use this bias factorFILE=HILLSa file in which the list of added hills is storedGRID_MIN=0.0,-1.0the lower bounds for the gridGRID_MAX=10.0,6.0the upper bounds for the gridPrint quantities to a file. More detailsARG=p1.s,p1.z,metathe input for this action is the scalar output from one or more other actionsSTRIDE=625the frequency with which the quantities of interest should be outputFILE=colvar2the name of the file on which to output these quantitiesENDPLUMEDTerminate plumed input. More details