Project ID: plumID:22.040
Source: mw-wtmeta-omi/plumed.dat
Originally used with PLUMED version: 2.8.0
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
tested onv2.9
tested onmaster
#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
=5259,5261,5270,5271,5272,5274,5289,5290,5291,5293,5303,5304,5305,5307,5317,5318,5319,5321,5336,5337,5338,5340,5346,5347,5348,5352,5360,5361,5362,5364,5380,5381,5382,5384,5392,5393,5394,5396,5407,5408,5409,5411,5423,5424,5425,5427,5443,5444,5445,5447,5456,5457,5458,5460,5466,5467,5468,5470,5480,5481,5482,5484,5504,5505,5506,5508,5524,5525,5526,5528,5534,5535,5536,5538,5545,5546,5547,5549,5561,5562,5563,5565,5582,5583,5584,5586,5592,5593,5594,5596,5616,5617,5618,5620,5630,5631,5632,5634,5654,5655,5656,5658,5676,5677,5678,5680,5700,5701,5702,5704,5719,5720,5721,5723,5730,5731,5732,5734,5744,5745,5746,5748,5754,5755,5756,5758,5770,5771,5772,5774,5780,5781,5782,5784,5792,5793,5794,5796,5813,5814,5815,5817,5824,5825,5826,5828,5840,5841,5842,5844,5859,5860,5861,5863,5880,5881,5882,5884,5894,5895,5896,5898,5913,5914,5915,5917,5923,5924,5925,5926,5937,5938,5939,5941,5957,5958,5959,5961,5977,5978,5979,5981,5991,5992,5993,5995,6011,6012,6013,6015,6033,6034,6035,6037,6043,6044,6045,6047,6064,6065,6066,6068,6071,6072,6073,6075,6087,6088,6089,6091,6098,6099,6100,6104,6112,6113,6114,6116,6126,6127,6128,6130,6148,6149,6150,6152,6167,6168,6169,6171,6181,6182,6183,6185,6193,6194,6195,6197,6212,6213,6214,6216,6222,6223,6224,6226,6242,6243,6244,6246,6256,6257,6258,6260,6270,6271,6272,6274,6286,6287,6288,6290,6307,6308,6309,6311,6317,6318,6319,6321,6329,6330,6331,6333,6340,6341,6342,6344,6360,6361,6362,6364,6376,6377,6378,6380,6395,6396,6397,6399,6419,6420,6421,6423,6426,6427,6428,6430,6438,6439,6440,6442,6453,6454,6455,6457,6469,6470,6471,6473,6493,6494,6495,6497,6510,6511,6512,6514,6529,6530,6531,6533,6539,6540,6541,6545,6553,6554,6555,6557,6560,6561,6562,6564,6577,6578,6579,6581,6591,6592,6593,6595,6598,6599,6600,6602,6612,6613,6614,6616,6631,6632,6633,6635,6641,6642,6643,6645,6653,6654,6655,6657,6674,6675,6676,6678,6688,6689,6690,6692,6709,6710,6711,6713,6731,6732,6733,6735,6750,6751,6752,6756,6764,6765,6766,6768,6776,6777,6778,6780,6788,6789,6790,6792,6808,6809,6810,6812,6822,6823,6824,6826,6829,6830,6831,6833,6839,6840,6841,6843,6855,6856,6857,6859,6874,6875,6876,6878,6884,6885,6886,6888,6908,6909,6910,6912,6922,6923,6924,6926,6933,6934,6935,6937,6947,6948,6949,6951,6969,6970,6971,6973,6988,6989,6990,6992,7000,7001,7002,7004,7011,7012,7013,7015,7033,7034,7035,7037,7049,7050,7051,7053,7060,7061,7062,7064,7067,7068,7069,7071,7081,7082,7083,7085,7102,7103,7104,7106,7116,7117,7118,7120,7137,7138,7139,7141,7156,7157,7158,7160,7177,7178,7179,7181,7201,7202,7203,7205,7220,7221,7222,7224,7240,7241,7242,7244,7264,7265,7266,7268,7286,7287,7288,7290,7297,7298,7299,7301,7311,7312,7313,7315,7330,7331,7332,7334,7352,7353,7354,7358,7366,7367,7368,7370,7386,7387,7388,7390,7401,7402,7403,7405,7425,7426,7427,7429,7437,7438,7439,7441,7456,7457,7458,7460,7467,7468,7469,7471,7481,7482,7483,7485,7496,7497,7498,7500,7515,7516,7517,7519,7536,7537,7538,7540,7553,7554,7555,7557,7563,7564,7565,7567,7570,7571,7572,7574,7584,7585,7586,7588,7606,7607,7608,7612,7620,7621,7622,7624,7630,7631,7632,7634,7644,7645,7646,7648,7651,7652,7653,7655,7667,7668,7669,7671,7677,7678,7679,7681,7684,7685,7686,7688,7704,7705,7706,7708,7718,7719,7720,7722,7728,7729,7730,7732,7749,7750,7751,7753,7769,7770,7771,7775,7783,7784,7785,7787,7802,7803,7804,7806,7826,7827,7828,7830,7837,7838,7839,7841,7858,7859,7860,7862,7869,7870,7871,7873,7889,7890,7891,7893,7913,7914,7915,7919,7927,7928,7929,7931,7941,7942,7943,7945,7962,7963,7964,7966,7969,7970,7971,7973,7985,7986,7987,7989,7992,7993,7994,7996,8009,8010,8011,8013,8026,8027,8028,8032,8040,8041,8042,8044,8061,8062,8063,8065,8085,8086,8087,8089,8101,8102,8103,8105,8117,8118,8119,8121,8133,8134,8135,8137,8152,8153,8154,8156,8163,8164,8165,8167,8183,8184,8185,8187,8198,8199,8200,8202,8217,8218,8219,8221,8236,8237,8238,8240,8253,8254,8255,8257,8263,8264,8265,8269,8277,8278,8279,8281,8287,8288,8289,8291,8301,8302,8303,8305,8317,8318,8319,8321,8327,8328,8329,8331,8334,8335,8336,8340,8348,8349,8350,8352,8370,8371,8372,8374,8392,8393,8394,8396,8403,8404

pca1: 
PCAVARS
Projection on principal component eigenvectors or other high dimensional linear subspace More details
 
REFERENCE
a pdb file containing the set of reference configurations
=ref-v1.pdb 
TYPE
 the manner in which distances are calculated
=SIMPLE 
pca2: 
PCAVARS
Projection on principal component eigenvectors or other high dimensional linear subspace More details
 
REFERENCE
a pdb file containing the set of reference configurations
=ref-v2.pdb 
TYPE
 the manner in which distances are calculated
=SIMPLE 

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
=pca1.eig-1,pca2.eig-1 
SIGMA
the widths of the Gaussian hills
=1.0,0.5 
HEIGHT
the heights of the Gaussian hills
=0.2 
PACE
the frequency for hill addition
=500 
# WALKERS_DIR=../HILLS WALKERS_N=18 WALKERS_ID=XXX WALKERS_RSTRIDE=50000 ##### uncomment this, create multiple directories, copy this file there, and adjust the path to REFERENCEs, change XXX to walker ID

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 

GRID_MIN
the lower bounds for the grid
=-40,-15 
GRID_MAX
the upper bounds for the grid
=20,25 
GRID_BIN
the number of bins for the grid
=150,150 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 
RCT_USTRIDE
the update stride for calculating the $c(t)$ reweighting factor
=1000 
... METAD

uw: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=pca1.eig-1,pca2.eig-1 
AT
the positions of the wall
=15,20 
KAPPA
the force constant for the wall
=500,500
lw: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=pca1.eig-1,pca2.eig-1 
AT
the positions of the wall
=-35,-12 
KAPPA
the force constant for the wall
=500,500

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=cv_all 
STRIDE
 the frequency with which the quantities of interest should be output
=500