Project ID: plumID:23.009
Source: chignolin/Distance_CV/TPI_deepTDA/plumed.dat
Originally used with PLUMED version: 2.9
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
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

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#  >> Chignolin <<
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#generated with gmx editconf -f topol.tpr -o reference.pdb, see https://www.plumed.org/doc-v2.7/user-doc/html/_m_o_l_i_n_f_o.html
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=chignolin-ref.pdb
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=1-166

# Define CVs

# Select Calpha
PROTEIN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-166
CA: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5,26,47,61,73,88,102,109,123,147
# RMSD
rmsd_ca: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=chignolin-ca.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
# END-TO-END DISTANCE
end: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,147
# HBONDS
hbonds: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=23,145 ATOMS2the atoms involved in each of the contacts you wish to calculate=45,120 ATOMS3the atoms involved in each of the contacts you wish to calculate=56,100 ATOMS4the atoms involved in each of the contacts you wish to calculate=56,107 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.4 NN=6 MM=8} SUM calculate the sum of all the contacts in the input
ene: ENERGYCalculate the total potential energy of the simulation box. More details

# Define descriptors
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-descriptors.dat

# Deep-LDA CV
# here deep.node-0 --> Deep-LDA 1
deepLDA: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=model_deep_lda_210distances.ptc ARGthe labels of the values from which the function is calculated=dd_1-54,dd_1-152,dd_5-7,dd_5-32,dd_5-52,dd_5-81,dd_5-121,dd_5-147,dd_5-158,dd_7-54,dd_7-81,dd_7-82,dd_7-145,dd_7-158,dd_10-52,dd_10-53,dd_10-135,dd_10-147,dd_11-22,dd_11-23,dd_11-54,dd_11-164,dd_11-165,dd_13-32,dd_13-54,dd_13-135,dd_15-18,dd_16-49,dd_18-164,dd_18-165,dd_20-22,dd_20-23,dd_20-32,dd_20-57,dd_20-99,dd_20-120,dd_20-131,dd_20-158,dd_20-165,dd_22-28,dd_22-53,dd_22-164,dd_23-54,dd_23-85,dd_23-92,dd_23-106,dd_23-145,dd_23-160,dd_23-164,dd_26-32,dd_26-55,dd_26-109,dd_26-139,dd_26-166,dd_28-125,dd_31-58,dd_31-63,dd_31-100,dd_31-115,dd_31-144,dd_32-36,dd_32-63,dd_32-66,dd_32-69,dd_34-105,dd_34-128,dd_36-70,dd_36-102,dd_36-105,dd_36-131,dd_36-133,dd_36-137,dd_36-144,dd_37-66,dd_37-69,dd_37-109,dd_39-83,dd_39-137,dd_41-63,dd_41-141,dd_41-144,dd_43-100,dd_43-105,dd_43-120,dd_44-120,dd_44-152,dd_45-47,dd_45-54,dd_45-75,dd_45-147,dd_47-78,dd_49-54,dd_49-71,dd_49-111,dd_49-119,dd_52-57,dd_52-66,dd_52-71,dd_52-83,dd_52-86,dd_52-94,dd_52-144,dd_53-55,dd_53-63,dd_53-69,dd_53-73,dd_53-102,dd_54-66,dd_54-81,dd_54-85,dd_54-120,dd_55-56,dd_55-58,dd_55-69,dd_55-70,dd_56-82,dd_56-105,dd_57-69,dd_57-102,dd_58-94,dd_58-99,dd_61-70,dd_61-71,dd_61-100,dd_61-107,dd_63-70,dd_63-83,dd_63-90,dd_63-105,dd_63-107,dd_63-120,dd_66-78,dd_66-83,dd_66-100,dd_66-107,dd_70-78,dd_70-102,dd_71-75,dd_71-92,dd_71-100,dd_73-88,dd_78-99,dd_78-141,dd_81-92,dd_82-90,dd_82-92,dd_82-94,dd_82-137,dd_83-92,dd_84-86,dd_84-94,dd_84-106,dd_86-98,dd_86-100,dd_88-111,dd_88-113,dd_90-99,dd_90-107,dd_90-109,dd_90-121,dd_90-141,dd_90-153,dd_92-113,dd_92-119,dd_98-107,dd_100-113,dd_102-105,dd_102-139,dd_102-141,dd_105-111,dd_105-123,dd_106-109,dd_106-166,dd_107-139,dd_109-131,dd_113-115,dd_113-121,dd_113-129,dd_113-135,dd_113-141,dd_115-135,dd_119-145,dd_121-125,dd_121-145,dd_125-143,dd_125-160,dd_128-143,dd_128-164,dd_129-134,dd_129-152,dd_129-155,dd_129-160,dd_131-137,dd_131-149,dd_131-162,dd_133-137,dd_133-165,dd_135-139,dd_135-141,dd_135-153,dd_135-158,dd_135-166,dd_137-166,dd_139-165,dd_141-158,dd_144-153,dd_147-155,dd_149-164,dd_149-165,dd_153-160

# Deep-TICA CVs
# here deep.node-0 --> Deep-TICA 1
deepTICA: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=model_deep_tica_210distances.ptc ARGthe labels of the values from which the function is calculated=dd_1-54,dd_1-152,dd_5-7,dd_5-32,dd_5-52,dd_5-81,dd_5-121,dd_5-147,dd_5-158,dd_7-54,dd_7-81,dd_7-82,dd_7-145,dd_7-158,dd_10-52,dd_10-53,dd_10-135,dd_10-147,dd_11-22,dd_11-23,dd_11-54,dd_11-164,dd_11-165,dd_13-32,dd_13-54,dd_13-135,dd_15-18,dd_16-49,dd_18-164,dd_18-165,dd_20-22,dd_20-23,dd_20-32,dd_20-57,dd_20-99,dd_20-120,dd_20-131,dd_20-158,dd_20-165,dd_22-28,dd_22-53,dd_22-164,dd_23-54,dd_23-85,dd_23-92,dd_23-106,dd_23-145,dd_23-160,dd_23-164,dd_26-32,dd_26-55,dd_26-109,dd_26-139,dd_26-166,dd_28-125,dd_31-58,dd_31-63,dd_31-100,dd_31-115,dd_31-144,dd_32-36,dd_32-63,dd_32-66,dd_32-69,dd_34-105,dd_34-128,dd_36-70,dd_36-102,dd_36-105,dd_36-131,dd_36-133,dd_36-137,dd_36-144,dd_37-66,dd_37-69,dd_37-109,dd_39-83,dd_39-137,dd_41-63,dd_41-141,dd_41-144,dd_43-100,dd_43-105,dd_43-120,dd_44-120,dd_44-152,dd_45-47,dd_45-54,dd_45-75,dd_45-147,dd_47-78,dd_49-54,dd_49-71,dd_49-111,dd_49-119,dd_52-57,dd_52-66,dd_52-71,dd_52-83,dd_52-86,dd_52-94,dd_52-144,dd_53-55,dd_53-63,dd_53-69,dd_53-73,dd_53-102,dd_54-66,dd_54-81,dd_54-85,dd_54-120,dd_55-56,dd_55-58,dd_55-69,dd_55-70,dd_56-82,dd_56-105,dd_57-69,dd_57-102,dd_58-94,dd_58-99,dd_61-70,dd_61-71,dd_61-100,dd_61-107,dd_63-70,dd_63-83,dd_63-90,dd_63-105,dd_63-107,dd_63-120,dd_66-78,dd_66-83,dd_66-100,dd_66-107,dd_70-78,dd_70-102,dd_71-75,dd_71-92,dd_71-100,dd_73-88,dd_78-99,dd_78-141,dd_81-92,dd_82-90,dd_82-92,dd_82-94,dd_82-137,dd_83-92,dd_84-86,dd_84-94,dd_84-106,dd_86-98,dd_86-100,dd_88-111,dd_88-113,dd_90-99,dd_90-107,dd_90-109,dd_90-121,dd_90-141,dd_90-153,dd_92-113,dd_92-119,dd_98-107,dd_100-113,dd_102-105,dd_102-139,dd_102-141,dd_105-111,dd_105-123,dd_106-109,dd_106-166,dd_107-139,dd_109-131,dd_113-115,dd_113-121,dd_113-129,dd_113-135,dd_113-141,dd_115-135,dd_119-145,dd_121-125,dd_121-145,dd_125-143,dd_125-160,dd_128-143,dd_128-164,dd_129-134,dd_129-152,dd_129-155,dd_129-160,dd_131-137,dd_131-149,dd_131-162,dd_133-137,dd_133-165,dd_135-139,dd_135-141,dd_135-153,dd_135-158,dd_135-166,dd_137-166,dd_139-165,dd_141-158,dd_144-153,dd_147-155,dd_149-164,dd_149-165,dd_153-160

#Deep-TDA CV
TPIdeepTDA: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=chignolin_distances_three_states_model.pt ARGthe labels of the values from which the function is calculated=dd_1-54,dd_1-152,dd_5-7,dd_5-32,dd_5-52,dd_5-81,dd_5-121,dd_5-147,dd_5-158,dd_7-54,dd_7-81,dd_7-82,dd_7-145,dd_7-158,dd_10-52,dd_10-53,dd_10-135,dd_10-147,dd_11-22,dd_11-23,dd_11-54,dd_11-164,dd_11-165,dd_13-32,dd_13-54,dd_13-135,dd_15-18,dd_16-49,dd_18-164,dd_18-165,dd_20-22,dd_20-23,dd_20-32,dd_20-57,dd_20-99,dd_20-120,dd_20-131,dd_20-158,dd_20-165,dd_22-28,dd_22-53,dd_22-164,dd_23-54,dd_23-85,dd_23-92,dd_23-106,dd_23-145,dd_23-160,dd_23-164,dd_26-32,dd_26-55,dd_26-109,dd_26-139,dd_26-166,dd_28-125,dd_31-58,dd_31-63,dd_31-100,dd_31-115,dd_31-144,dd_32-36,dd_32-63,dd_32-66,dd_32-69,dd_34-105,dd_34-128,dd_36-70,dd_36-102,dd_36-105,dd_36-131,dd_36-133,dd_36-137,dd_36-144,dd_37-66,dd_37-69,dd_37-109,dd_39-83,dd_39-137,dd_41-63,dd_41-141,dd_41-144,dd_43-100,dd_43-105,dd_43-120,dd_44-120,dd_44-152,dd_45-47,dd_45-54,dd_45-75,dd_45-147,dd_47-78,dd_49-54,dd_49-71,dd_49-111,dd_49-119,dd_52-57,dd_52-66,dd_52-71,dd_52-83,dd_52-86,dd_52-94,dd_52-144,dd_53-55,dd_53-63,dd_53-69,dd_53-73,dd_53-102,dd_54-66,dd_54-81,dd_54-85,dd_54-120,dd_55-56,dd_55-58,dd_55-69,dd_55-70,dd_56-82,dd_56-105,dd_57-69,dd_57-102,dd_58-94,dd_58-99,dd_61-70,dd_61-71,dd_61-100,dd_61-107,dd_63-70,dd_63-83,dd_63-90,dd_63-105,dd_63-107,dd_63-120,dd_66-78,dd_66-83,dd_66-100,dd_66-107,dd_70-78,dd_70-102,dd_71-75,dd_71-92,dd_71-100,dd_73-88,dd_78-99,dd_78-141,dd_81-92,dd_82-90,dd_82-92,dd_82-94,dd_82-137,dd_83-92,dd_84-86,dd_84-94,dd_84-106,dd_86-98,dd_86-100,dd_88-111,dd_88-113,dd_90-99,dd_90-107,dd_90-109,dd_90-121,dd_90-141,dd_90-153,dd_92-113,dd_92-119,dd_98-107,dd_100-113,dd_102-105,dd_102-139,dd_102-141,dd_105-111,dd_105-123,dd_106-109,dd_106-166,dd_107-139,dd_109-131,dd_113-115,dd_113-121,dd_113-129,dd_113-135,dd_113-141,dd_115-135,dd_119-145,dd_121-125,dd_121-145,dd_125-143,dd_125-160,dd_128-143,dd_128-164,dd_129-134,dd_129-152,dd_129-155,dd_129-160,dd_131-137,dd_131-149,dd_131-162,dd_133-137,dd_133-165,dd_135-139,dd_135-141,dd_135-153,dd_135-158,dd_135-166,dd_137-166,dd_139-165,dd_141-158,dd_144-153,dd_147-155,dd_149-164,dd_149-165,dd_153-160

#HLDA
d1: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=23,146 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d2: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=120,46 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d3: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=56,101 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d4: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=56,108 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d5: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=87,101 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.15 D_0=0.08 NN=6 MM=8}
d6: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=72,87 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.12 D_0=0.17 NN=6 MM=8}

hlda: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1.contact-1,d2.contact-1,d3.contact-1,d4.contact-1,d5.contact-1,d6.contact-1 COEFFICIENTS the coefficients of the arguments in your function=0.6188,0.5975,0.5045,-0.0708,0.0217,0.0140 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act=TPIdeepTDA.node-0
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=40
  SIGMA the initial widths of the kernels=0.2
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
... OPES_METAD



# PRINT
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=hlda,rmsd_ca,deepLDA.node-0,deepTICA.node-0,TPIdeepTDA.node-0,opes.bias FILEthe name of the file on which to output these quantities=COLVARb
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 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=COLVAR