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 onv2.10
tested onmaster
#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=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: PCAVARSProjection on principal component eigenvectors or other high dimensional linear subspace This action is a shortcut. More details REFERENCEa pdb file containing the set of reference configurations=ref-v1.pdb TYPE the manner in which distances are calculated=SIMPLE 
pca2: PCAVARSProjection on principal component eigenvectors or other high dimensional linear subspace This action is a shortcut. More details REFERENCEa pdb file containing the set of reference configurations=ref-v2.pdb TYPE the manner in which distances are calculated=SIMPLE 

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=meta
ARGthe labels of the scalars on which the bias will act=pca1.eig-1,pca2.eig-1 SIGMAthe widths of the Gaussian hills=1.0,0.5 HEIGHTthe heights of the Gaussian hills=0.2 PACEthe 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
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 
GRID_MINthe lower bounds for the grid=-40,-15 GRID_MAXthe upper bounds for the grid=20,25 GRID_BINthe 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_USTRIDEthe update stride for calculating the c(t) reweighting factor=1000 
... METAD

uw: UPPER_WALLSDefines a wall for the value of one or more collective variables, This action is a shortcut and it has hidden defaults. More details ARGthe arguments on which the bias is acting=pca1.eig-1,pca2.eig-1 ATthe positions of the wall=15,20 KAPPAthe force constant for the wall=500,500
lw: LOWER_WALLSDefines a wall for the value of one or more collective variables, This action is a shortcut and it has hidden defaults. More details ARGthe arguments on which the bias is acting=pca1.eig-1,pca2.eig-1 ATthe positions of the wall=-35,-12 KAPPAthe force constant for the wall=500,500

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe 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