PLUMED-NEST

Project ID: plumID:20.006
Source: metad_GCGR-GPR/plumed.dat
Originally used with PLUMED version: 2.4.3
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

# Tue Jul 10 16:10:33 CEST 2018
#RESTART
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=5,22,33,50,57,71,91,105,116,128,149,160,182,203,222,234,245,269,293,303,320,332,352,368,385,409,428,445,459,476,493,509,526,538,558,577,597,612,634,658,680,699,720,727,739,756,766,784,802,816,835,846,865,892,906,920,926,940,955,974,990,1000,1014,1038,1052,1072,1084,1106,1127,1138,1148,1180,1186,1198,1220,1226,1236,1250,1264,1278,1288,1302,1321,1332,1350,1356,1380,1401,1428,1434,1458,1476,1494,1516,1532,1549,1567,1591,1611,1627,1647,1669,1693,1703,1718,1724,1736,1743,1760,1784,1800,1824,1839,1845,1869,1876,1901,1907,1931,1955,1967,1977,1988,2005,2015,2032,2049,2061,2068,2083,2098,2117,2132,2148,2165,2187,2202,2218,2228,2250,2267,2288,2299,2310,2330,2347,2363,2380,2401,2415,2431,2438,2459,2470,2489,2500,2519,2526,2536,2555,2574,2593,2603,2622,2632,2651,2670,2677,2684,2703,2714,2736,2755,2772,2783,2797,2821,2835,2845,2864,2881,2891,2905,2924,2944,2954,2965,2985,3001,3020,3042,3052,3063,3074,3090,3109,3125,3144,3156,3163,3182,3201,3225,3239,3263,3284,3295,3312,3334,3353,3360,3372,3384,3403,3414,3430,3441,3455,3479,3498,3509,3521,3528,3538,3554,3564,3571,3581,3605,3621,3631,3641,3657,3677,3694,3711,3732,3739,3758,3774,3784,3798,3819,3830,3854,3873,3892,3908,3923,3930,3949,3970,3989,4006,4020,4039,4058,4065,4084,4094,4108,4135,4141,4156,4180,4191,4211,4231,4242,4261,4282,4301,4308,4327,4334,4358,4365,4383,4389,4406,4425,4445,4461,4485,4491,4515,4525,4541,4557,4579,4590,4609,4629,4644,4658,4674,4691,4701,4725,4739,4750,4764,4776,4790,4807,4814,4834,4858,4882,4901,4920,4944,4972,4978,4994,5014,5033,5043,5062,5081,5100,5114,5134,5154,5173,5193,5209,5233,5252,5268,5285,5304,5323,5339,5349,5371,5390,5414,5424,5448,5465,5482,5500,5517,5531,5543,5564,5586,5606,5630,5649,5659,5681,5692,5706,5725,5739,5758,5785,5791,5810,5829,5836,5852,5869,5884,5900,5916,5936,5946,5966,5982,5996,6008,6023,6040,6050,6067,6074,6088,6107,6131,6142,6152,6174,6193,6213,6233,6245,6264,6284,6303,6314,6325,6345,6362,6369,6388,6407,6423,6433,6449,6468,6489,6500,6520,6539,6553,6575,6590,6606,6623,6634,6649,6668,6692,6716,6740,6764,6781,6805,6829,6853,6872,6879,6901,6917,6936,6960,6978,6992,7007,7019,7036,7060,7074,7089,7104,7126,7136,7153,7177,7192,7202,7216,7238,7260,7279,7294,7316,7333,7352,7369,7391,7403,7425,7442,7458,7479,7503,7513,7527,7544,7568,7587,7606,7625,7644,7651,7661,7668,7683,7694,7701,7723,7734,7748,7767,7783,7805,7822,7839,7863,7882,7901,7918,7934,7948,7955,7975,7989,7996,8008,8019,8034,8056,8066,8080,8102,8118,8135,8147,8166,8188,8202,8216,8235,8257,8272,8282,8301,8316,8330,8349,8365,8375,8385,8402,8413,8427,8446,8470,8484,8490,8506,8521,8540,8550,8572,8578,8593,8607,8624,8644,8668,8684,8696,8717,8736,8755,8766,8782,8799,8813,8837,8843,8855,8875,8887,8915,8929,8935,8950,8970,8991,9006,9023,9033,9055,9065,9084,9108,9123,9135,9150,9157,9173,9197,9207,9218,9239,9254,9278,9289,9303,9318,9339,9356,9375,9394,9406,9417,9427,9444,9465,9485,9504,9516,9538,9557,9569,9585,9604,9626,9643,9655,9667,9688,9712,9718,9729,9741,9758,9770,9789,9808,9832,9843,9867,9883,9902,9916,9927,9934,9953,9973,9988,10002,10024,10044,10061,10077,10089,10111,10127,10141,10161,10178,10195,10215,10227,10243,10250,10257,10274,10298,10310,10325,10349,10373,10395,10419,10438,10455,10466,10486,10500,10512,10528,10542,10552,10571,10590,10610,10626,10642,10652,10663,10674,10685,10706,10720,10737,10753,10772,10796,10811,10823,10837,10854,10868,10882,10906,10925,10942,10957,10967,10986,11000,11019,11039,11061,11072,11091,11115,11129,11143,11167,11191,11210,11234,11248,11267,11278,11294,11313,11332,11352,11371,11385,11407,11424,11436,11455,11474,11484,11499,11521,11537,11556,11566,11573,11595,11606,11628,11647,11662,11674,11695,11723,11729,11744,11764,11774,11798,11819,11833,11855,11861,11876,11888,11898,11920,11926,11949,11955,11962,11977,11997,12003,12027,12043,12057,12081,12091,12113,12134,12154,12173,12197,12209,12224,12244,12263,12287,12306,12317,12331,12341,12352,12359,12371,12378,12402,12420,12441,12452,12481,12487,12504,12524,12538,12549,12559,12575,12587,12601,12616,12630,12649,12673,12697,12713,12733,12747,12759,12770,12794,12806,12825,12844,12861,12885,12902,12919,12938,12962,12979,13000,13015,13034

The WHOLEMOLECULES action with label  calculates somethinghetxThe CENTER_FAST action with label hetx calculates the following quantities:
 Quantity   
 Type   
 Description  
hetx
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=2864,3908,6468
coupThe DISTANCE action with label coup calculates the following quantities:
 Quantity   
 Type   
 Description  
coup.x
scalar
the x-component of the vector connecting the two atoms
coup.y
scalar
the y-component of the vector connecting the two atoms
coup.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=hetx,12979 COMPONENTS calculate the x, y and z components of the distance separately and store them as label

openThe RMSD action with label open calculates the following quantities:
 Quantity   
 Type   
 Description  
open
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.open.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
open: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.open.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
closedThe RMSD action with label closed calculates the following quantities:
 Quantity   
 Type   
 Description  
closed
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.closed.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
closed: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.closed.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
linkThe DISTANCE action with label link calculates the following quantities:
 Quantity   
 Type   
 Description  
link
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6978,28028

COMBINECalculate a polynomial combination of a set of other variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=progThe COMBINE action with label prog calculates the following quantities:
 Quantity   
 Type   
 Description  
prog
scalar
a linear compbination
  ARGthe values input to this function=open,closed
  COEFFICIENTS the coefficients of the arguments in your function=1,-1
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

COMBINECalculate a polynomial combination of a set of other variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=distThe COMBINE action with label dist calculates the following quantities:
 Quantity   
 Type   
 Description  
dist
scalar
a linear compbination
  ARGthe values input to this function=open,closed
  COEFFICIENTS the coefficients of the arguments in your function=1,1
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

METADUsed to performed metadynamics on one or more collective variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential
  ARGthe labels of the scalars on which the bias will act=prog,dist,coup.z
  SIGMAthe widths of the Gaussian hills=0.05,0.05,0.05 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=500
  BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
  GRID_MINthe lower bounds for the grid=-1.2,0.5,-0.75 GRID_MAXthe upper bounds for the grid=1.2,2.0,3.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.025,0.025,0.025
  FILE a file in which the list of added hills is stored=HILLS
# WALKERS_MPI
... METAD

MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=radThe MATHEVAL action with label rad calculates the following quantities:
 Quantity   
 Type   
 Description  
rad
scalar
an arbitrary function
ARGthe values input to this function=coup.x,coup.y
VARthe names to give each of the arguments in the function=x,y
FUNCthe function you wish to evaluate=sqrt(x*x+y*y)
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
  ARGthe arguments on which the bias is acting=open,closed,coup.z,rad,link,dist
  ATthe positions of the wall=1.2,1.2,2.5,1.5,0.5,1.6
  KAPPAthe force constant for the wall=5000.0,5000.0,3000.0,3000.0,1000.0,3000.0
... UPPER_WALLS

LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
  ARGthe arguments on which the bias is acting=coup.z
  ATthe positions of the wall=0.0
  KAPPAthe force constant for the wall=3000.0
... LOWER_WALLS

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f