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
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the 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

hetx: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2864,3908,6468
coup: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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

The DISTANCE action with label coup calculates the following quantities:
 Quantity   
 Description  
coup.x
the x-component of the vector connecting the two atoms
coup.y
the y-component of the vector connecting the two atoms
coup.z
the z-component of the vector connecting the two atomsopen: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a 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
closed: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a 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
link: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6978,28028

The DISTANCE action with label link calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=prog
  
ARG
the input to this function
=open,closed
  
COEFFICIENTS
 the coefficients of the arguments in your function
=1,-1
  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dist
  
ARG
the input to this function
=open,closed
  
COEFFICIENTS
 the coefficients of the arguments in your function
=1,1
  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=meta
  
ARG
the input for this action is the scalar output from one or more other actions
=prog,dist,coup.z
  
SIGMA
the widths of the Gaussian hills
=0.05,0.05,0.05 
HEIGHT
the heights of the Gaussian hills
=1.5 
PACE
the frequency for hill addition
=500
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
  
GRID_MIN
the lower bounds for the grid
=-1.2,0.5,-0.75 
GRID_MAX
the upper bounds for the grid
=1.2,2.0,3.0 
GRID_SPACING
the 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

The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potential
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rad
ARG
the input to this function
=coup.x,coup.y
VAR
the names to give each of the arguments in the function
=x,y
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL

UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall
  
ARG
the arguments on which the bias is acting
=open,closed,coup.z,rad,link,dist
  
AT
the positions of the wall
=1.2,1.2,2.5,1.5,0.5,1.6
  
KAPPA
the force constant for the wall
=5000.0,5000.0,3000.0,3000.0,1000.0,3000.0
... UPPER_WALLS

LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall
  
ARG
the arguments on which the bias is acting
=coup.z
  
AT
the positions of the wall
=0.0
  
KAPPA
the force constant for the wall
=3000.0
... LOWER_WALLS

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%8.4f