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
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
The WHOLEMOLECULES action with label calculates somethingpca1The PCAVARS action with label pca1 calculates the following quantities:| Quantity | Type | Description |
| pca1_eig | vector | the projections on the eigenvalues |
| pca1_residual | scalar | the residual distance that is not projected on any of the eigenvalues |
: 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
# pca1: PCAVARS REFERENCE=ref-v1.pdb TYPE=SIMPLE
The PCAVARS action with label pca1 calculates the following quantities:| Quantity | Description |
| pca1.eig | the projections on the eigenvalues |
| pca1.residual | the residual distance that is not projected on any of the eigenvalues |
pca1_atThe RMSD action with label pca1_at calculates the following quantities:| Quantity | Type | Description |
| pca1_at.dist | scalar | the RMSD distance the atoms have moved |
| pca1_at.disp | vector | the vector of displacements for the atoms |
: RMSDCalculate the RMSD with respect to a reference structure. More details DISPLACEMENT Calculate the vector of displacements instead of the length of this vector SQUARED This should be setted if you want MSD instead of RMSD NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=ref-v1.pdb TYPE the manner in which RMSD alignment is performed=SIMPLE
pca1_peigThe CONSTANT action with label pca1_peig calculates the following quantities:| Quantity | Type | Description |
| pca1_peig | matrix | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant 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NROWS the number of rows in your input matrix=1 NCOLS the number of columns in your matrix=2400
pca1_eigThe MATRIX_VECTOR_PRODUCT action with label pca1_eig calculates the following quantities:| Quantity | Type | Description |
| pca1_eig | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=pca1_peig,pca1_at.disp
pca1_eig-1The SELECT_WITH_MASK action with label pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| pca1_eig-1 | vector | a vector/matrix of values that is obtained using a mask to select elements of interest |
: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix More details ARGthe value from which we are selecting components=pca1_eig COMPONENTSthe components in the input value that you woul like to build a new vector from=1
pca1_eig2The CUSTOM action with label pca1_eig2 calculates the following quantities:| Quantity | Type | Description |
| pca1_eig2 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=pca1_eig FUNCthe function you wish to evaluate=x*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
pca1_eigsum2The SUM action with label pca1_eigsum2 calculates the following quantities:| Quantity | Type | Description |
| pca1_eigsum2 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=pca1_eig2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
pca1_residualThe CUSTOM action with label pca1_residual calculates the following quantities:| Quantity | Type | Description |
| pca1_residual | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=pca1_at.dist,pca1_eigsum2 FUNCthe function you wish to evaluate=sqrt(x-y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
metaThe METAD action with label meta calculates the following quantities:| Quantity | Type | Description |
| meta.bias | scalar | the instantaneous value of the bias potential |
| meta.rbias | scalar | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram. |
| meta.rct | scalar | the reweighting factor c(t). |
: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=pca1.eig-1 SIGMAthe widths of the Gaussian hills=2.0 HEIGHTthe heights of the Gaussian hills=0.03 PACEthe frequency for hill addition=1000 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=-50 GRID_MAXthe upper bounds for the grid=20 GRID_BINthe 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]
meta: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=pca1.eig-1 SIGMAthe widths of the Gaussian hills=2.0 HEIGHTthe heights of the Gaussian hills=0.03 PACEthe frequency for hill addition=1000 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=-50 GRID_MAXthe upper bounds for the grid=20 GRID_BINthe 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] FILE a file in which the list of added hills is stored=HILLS
uwThe UPPER_WALLS action with label uw calculates the following quantities:| Quantity | Type | Description |
| uw_bias | scalar | the instantaneous value of the bias potential |
| uw_force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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 ATthe positions of the wall=20 KAPPAthe force constant for the wall=35000
The UPPER_WALLS action with label uw calculates the following quantities:| Quantity | Description |
| uw.bias | the instantaneous value of the bias potential |
| uw.force2 | the instantaneous value of the squared force due to this bias potential |
uw: UPPER_WALLSDefines a wall for the value of one or more collective variables, This action is a shortcut and uses the defaults shown here. More details ARGthe arguments on which the bias is acting=pca1.eig-1 ATthe positions of the wall=20 KAPPAthe force constant for the wall=35000 OFFSET the offset for the start of the wall=0.0 EPS the values for s_i in the expression for a wall=1.0 EXP the powers for the walls=2.0
# uw: UPPER_WALLS ARG=pca1.eig-1 AT=20 KAPPA=35000
uw_cv_pca1_eig-1The COMBINE action with label uw_cv_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_cv_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=pca1.eig-1 PARAMETERS the parameters of the arguments in your function=20
uw_scale_pca1_eig-1The CUSTOM action with label uw_scale_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_scale_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(x+0.0)/1.0 ARGthe values input to this function=uw_cv_pca1_eig-1
uw_pow_pca1_eig-1The CUSTOM action with label uw_pow_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_pow_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=step(x)*x^2.0 ARGthe values input to this function=uw_scale_pca1_eig-1
uw_v_wall_pca1_eig-1The CUSTOM action with label uw_v_wall_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_v_wall_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=35000*x ARGthe values input to this function=uw_pow_pca1_eig-1
uw_wall_pca1_eig-1The SUM action with label uw_wall_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_wall_pca1_eig-1 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=uw_v_wall_pca1_eig-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
uw_force_pca1_eig-1The CUSTOM action with label uw_force_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_force_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=35000*2.0*x/(y*1.0) ARGthe values input to this function=uw_pow_pca1_eig-1,uw_scale_pca1_eig-1
uw_v_force2_pca1_eig-1The CUSTOM action with label uw_v_force2_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_v_force2_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=x*x ARGthe values input to this function=uw_force_pca1_eig-1
uw_force2_pca1_eig-1The SUM action with label uw_force2_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| uw_force2_pca1_eig-1 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=uw_v_force2_pca1_eig-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
uw_biasThe COMBINE action with label uw_bias calculates the following quantities:| Quantity | Type | Description |
| uw_bias | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=uw_wall_pca1_eig-1
BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=uw_bias
uw_force2The COMBINE action with label uw_force2 calculates the following quantities:| Quantity | Type | Description |
| uw_force2 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=uw_force2_pca1_eig-1
# --- End of included input --- lwThe LOWER_WALLS action with label lw calculates the following quantities:| Quantity | Type | Description |
| lw_bias | scalar | the instantaneous value of the bias potential |
| lw_force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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 ATthe positions of the wall=-47 KAPPAthe force constant for the wall=5000
The LOWER_WALLS action with label lw calculates the following quantities:| Quantity | Description |
| lw.bias | the instantaneous value of the bias potential |
| lw.force2 | the instantaneous value of the squared force due to this bias potential |
lw: LOWER_WALLSDefines a wall for the value of one or more collective variables, This action is a shortcut and uses the defaults shown here. More details ARGthe arguments on which the bias is acting=pca1.eig-1 ATthe positions of the wall=-47 KAPPAthe force constant for the wall=5000 OFFSET the offset for the start of the wall=0.0 EPS the values for s_i in the expression for a wall=1.0 EXP the powers for the walls=2.0
# lw: LOWER_WALLS ARG=pca1.eig-1 AT=-47 KAPPA=5000
lw_cv_pca1_eig-1The COMBINE action with label lw_cv_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_cv_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=pca1.eig-1 PARAMETERS the parameters of the arguments in your function=-47
lw_scale_pca1_eig-1The CUSTOM action with label lw_scale_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_scale_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(x-0.0)/1.0 ARGthe values input to this function=lw_cv_pca1_eig-1
lw_pow_pca1_eig-1The CUSTOM action with label lw_pow_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_pow_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=step(-x)*(-x)^2.0 ARGthe values input to this function=lw_scale_pca1_eig-1
lw_v_wall_pca1_eig-1The CUSTOM action with label lw_v_wall_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_v_wall_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=5000*x ARGthe values input to this function=lw_pow_pca1_eig-1
lw_wall_pca1_eig-1The SUM action with label lw_wall_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_wall_pca1_eig-1 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lw_v_wall_pca1_eig-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lw_force_pca1_eig-1The CUSTOM action with label lw_force_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_force_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=5000*2.0*x/(y*1.0) ARGthe values input to this function=lw_pow_pca1_eig-1,lw_scale_pca1_eig-1
lw_v_force2_pca1_eig-1The CUSTOM action with label lw_v_force2_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_v_force2_pca1_eig-1 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=x*x ARGthe values input to this function=lw_force_pca1_eig-1
lw_force2_pca1_eig-1The SUM action with label lw_force2_pca1_eig-1 calculates the following quantities:| Quantity | Type | Description |
| lw_force2_pca1_eig-1 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=lw_v_force2_pca1_eig-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
lw_biasThe COMBINE action with label lw_bias calculates the following quantities:| Quantity | Type | Description |
| lw_bias | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lw_wall_pca1_eig-1
BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=lw_bias
lw_force2The COMBINE action with label lw_force2 calculates the following quantities:| Quantity | Type | Description |
| lw_force2 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lw_force2_pca1_eig-1
# --- End of included input ---
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=5000
