Project ID: plumID:22.040
Source: mw-wtmeta-wt/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
=5243,5245,5254,5255,5256,5258,5273,5274,5275,5277,5287,5288,5289,5291,5301,5302,5303,5305,5320,5321,5322,5324,5330,5331,5332,5336,5344,5345,5346,5348,5364,5365,5366,5368,5371,5372,5373,5375,5386,5387,5388,5390,5402,5403,5404,5406,5422,5423,5424,5426,5435,5436,5437,5439,5445,5446,5447,5449,5459,5460,5461,5463,5483,5484,5485,5487,5503,5504,5505,5507,5513,5514,5515,5517,5524,5525,5526,5528,5540,5541,5542,5544,5561,5562,5563,5565,5571,5572,5573,5575,5595,5596,5597,5599,5609,5610,5611,5613,5633,5634,5635,5637,5655,5656,5657,5659,5679,5680,5681,5683,5698,5699,5700,5702,5709,5710,5711,5713,5723,5724,5725,5727,5733,5734,5735,5737,5749,5750,5751,5753,5759,5760,5761,5763,5771,5772,5773,5775,5792,5793,5794,5796,5803,5804,5805,5807,5819,5820,5821,5823,5838,5839,5840,5842,5859,5860,5861,5863,5873,5874,5875,5877,5884,5885,5886,5888,5894,5895,5896,5898,5905,5906,5907,5909,5925,5926,5927,5929,5936,5937,5938,5940,5950,5951,5952,5954,5970,5971,5972,5974,5992,5993,5994,5996,6002,6003,6004,6006,6023,6024,6025,6027,6030,6031,6032,6034,6046,6047,6048,6050,6057,6058,6059,6063,6071,6072,6073,6075,6085,6086,6087,6089,6107,6108,6109,6111,6126,6127,6128,6130,6140,6141,6142,6144,6152,6153,6154,6156,6171,6172,6173,6175,6181,6182,6183,6185,6201,6202,6203,6205,6215,6216,6217,6219,6229,6230,6231,6233,6245,6246,6247,6249,6266,6267,6268,6270,6276,6277,6278,6280,6288,6289,6290,6292,6299,6300,6301,6303,6319,6320,6321,6323,6335,6336,6337,6339,6354,6355,6356,6358,6378,6379,6380,6382,6385,6386,6387,6389,6397,6398,6399,6401,6412,6413,6414,6416,6428,6429,6430,6432,6452,6453,6454,6456,6469,6470,6471,6473,6488,6489,6490,6492,6498,6499,6500,6504,6512,6513,6514,6516,6519,6520,6521,6523,6536,6537,6538,6540,6550,6551,6552,6554,6557,6558,6559,6561,6579,6580,6581,6583,6598,6599,6600,6602,6608,6609,6610,6612,6620,6621,6622,6624,6641,6642,6643,6645,6655,6656,6657,6659,6676,6677,6678,6680,6698,6699,6700,6702,6717,6718,6719,6723,6731,6732,6733,6735,6743,6744,6745,6747,6755,6756,6757,6759,6775,6776,6777,6779,6789,6790,6791,6793,6796,6797,6798,6800,6806,6807,6808,6810,6822,6823,6824,6826,6841,6842,6843,6845,6851,6852,6853,6855,6875,6876,6877,6879,6889,6890,6891,6893,6900,6901,6902,6904,6914,6915,6916,6918,6928,6929,6930,6932,6947,6948,6949,6951,6959,6960,6961,6963,6970,6971,6972,6974,6992,6993,6994,6996,7008,7009,7010,7012,7015,7016,7017,7019,7022,7023,7024,7026,7036,7037,7038,7040,7057,7058,7059,7061,7071,7072,7073,7075,7092,7093,7094,7096,7111,7112,7113,7115,7132,7133,7134,7136,7156,7157,7158,7160,7175,7176,7177,7179,7195,7196,7197,7199,7219,7220,7221,7223,7241,7242,7243,7245,7252,7253,7254,7256,7266,7267,7268,7270,7285,7286,7287,7289,7307,7308,7309,7313,7321,7322,7323,7325,7341,7342,7343,7345,7356,7357,7358,7360,7380,7381,7382,7384,7392,7393,7394,7396,7411,7412,7413,7415,7422,7423,7424,7426,7436,7437,7438,7440,7451,7452,7453,7455,7470,7471,7472,7474,7491,7492,7493,7495,7508,7509,7510,7512,7518,7519,7520,7522,7525,7526,7527,7529,7536,7537,7538,7540,7550,7551,7552,7556,7564,7565,7566,7568,7574,7575,7576,7578,7588,7589,7590,7592,7595,7596,7597,7599,7611,7612,7613,7615,7626,7627,7628,7630,7633,7634,7635,7637,7653,7654,7655,7657,7667,7668,7669,7671,7677,7678,7679,7681,7698,7699,7700,7702,7718,7719,7720,7724,7732,7733,7734,7736,7751,7752,7753,7755,7768,7769,7770,7772,7779,7780,7781,7783,7800,7801,7802,7804,7807,7808,7809,7811,7827,7828,7829,7831,7844,7845,7846,7850,7858,7859,7860,7862,7872,7873,7874,7876,7886,7887,7888,7890,7893,7894,7895,7897,7909,7910,7911,7913,7916,7917,7918,7920,7937,7938,7939,7941,7954,7955,7956,7960,7968,7969,7970,7972,7989,7990,7991,7993,8013,8014,8015,8017,8029,8030,8031,8033,8045,8046,8047,8049,8061,8062,8063,8065,8080,8081,8082,8084,8091,8092,8093,8095,8111,8112,8113,8115,8126,8127,8128,8130,8145,8146,8147,8149,8164,8165,8166,8168,8181,8182,8183,8185,8191,8192,8193,8197,8205,8206,8207,8209,8215,8216,8217,8219,8229,8230,8231,8233,8245,8246,8247,8249,8255,8256,8257,8259,8262,8263,8264,8268,8276,8277,8278,8280,8298,8299,8300,8302,8320,8321,8322,8324,8331,8332
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
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