Project ID: plumID:22.040
Source: ktr-meta-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
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

meta: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=pca1.eig-1 
SIGMA
the widths of the Gaussian hills
=2.0 
HEIGHT
the heights of the Gaussian hills
=0.03 
PACE
the frequency for hill addition
=1000 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
GRID_MIN
the lower bounds for the grid
=-50 
GRID_MAX
the upper bounds for the grid
=20 
GRID_BIN
the number of bins for the grid
=150 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]


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 
AT
the positions of the wall
=20  
KAPPA
the force constant for the wall
=35000 
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 
AT
the positions of the wall
=-47 
KAPPA
the force constant for the wall
=5000

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
=5000