Project ID: plumID:23.009
Source: chignolin/Contact_CV/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
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
#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.htmlMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=chignolin-ref.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-166the atoms that make up a molecule that you wish to align
# 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 detailsATOMS=1-166 CA:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=5,26,47,61,73,88,102,109,123,147 # RMSD rmsd_ca:the numerical indexes for the set of atoms in the groupRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=chignolin-ca.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL # END-TO-END DISTANCE end:the manner in which RMSD alignment is performedDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,147 # HBONDS hbonds:the pair of atom that we are calculating the distance betweenCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=23,145the atoms involved in each of the contacts you wish to calculateATOMS2=45,120the atoms involved in each of the contacts you wish to calculateATOMS3=56,100the atoms involved in each of the contacts you wish to calculateATOMS4=56,107the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.4 NN=6 MM=8}The switching functions to use for each of the contacts in your mapSUMene:calculate the sum of all the contacts in the inputENERGYCalculate the total potential energy of the simulation box. More details
# Define descriptorsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=plumed-descriptors.datfile to be included
# Deep-LDA CV # here deep.node-0 --> Deep-LDA 1 deepLDA:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=model_deep_lda_210distances.ptcFilename of the PyTorch compiled modelARG=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_153-160the input for this action is the scalar output from one or more other actions
# Deep-TICA CVs # here deep.node-0 --> Deep-TICA 1 deepTICA:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=model_deep_tica_210distances.ptcFilename of the PyTorch compiled modelARG=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_153-160the input for this action is the scalar output from one or more other actions
#c-alpha-contacts: cont1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=26Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont2:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=47Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont3:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=61Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont4:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=73Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont5:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=88Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont6:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=102Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont7:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=109Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont8:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont9:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont10:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=47Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont11:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=61Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont12:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=73Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont13:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=88Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont14:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=102Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont15:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=109Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont16:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont17:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=26First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont18:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=47First list of atomsGROUPB=61Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont19:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=47First list of atomsGROUPB=73Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont20:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=47First list of atomsGROUPB=88Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont21:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=47First list of atomsGROUPB=102Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont22:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=47First list of atomsGROUPB=109Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont23:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=47First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont24:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=47First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont25:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=61First list of atomsGROUPB=73Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont26:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=61First list of atomsGROUPB=88Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont27:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=61First list of atomsGROUPB=102Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont28:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=61First list of atomsGROUPB=109Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont29:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=61First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont30:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=61First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont31:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=73First list of atomsGROUPB=88Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont32:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=73First list of atomsGROUPB=102Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont33:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=73First list of atomsGROUPB=109Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont34:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=73First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont35:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=73First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont36:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=88First list of atomsGROUPB=102Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont37:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=88First list of atomsGROUPB=109Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont38:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=88First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont39:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=88First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont40:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=102First list of atomsGROUPB=109Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont41:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=102First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont42:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=102First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont43:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=109First list of atomsGROUPB=123Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont44:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=109First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12} cont45:This keyword is used if you want to employ an alternative to the continuous switching function defined aboveCOORDINATIONCalculate coordination numbers. More detailsGROUPA=123First list of atomsGROUPB=147Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}This keyword is used if you want to employ an alternative to the continuous switching function defined above
#Deep-TDA CV deepTDA:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=chignolin_contacts_two_states_model.ptFilename of the PyTorch compiled modelARG=cont1,cont2,cont3,cont4,cont5,cont6,cont7,cont8,cont9,cont10,cont11,cont12,cont13,cont14,cont15,cont16,cont17,cont18,cont19,cont20,cont21,cont22,cont23,cont24,cont25,cont26,cont27,cont28,cont29,cont30,cont31,cont32,cont33,cont34,cont35,cont36,cont37,cont38,cont39,cont40,cont41,cont42,cont43,cont44,cont45the input for this action is the scalar output from one or more other actions
#HLDA d1:CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=23,146the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8} d2:The switching functions to use for each of the contacts in your mapCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=120,46the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8} d3:The switching functions to use for each of the contacts in your mapCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=56,101the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8} d4:The switching functions to use for each of the contacts in your mapCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=56,108the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8} d5:The switching functions to use for each of the contacts in your mapCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=87,101the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.15 D_0=0.08 NN=6 MM=8} d6:The switching functions to use for each of the contacts in your mapCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=72,87the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=0.12 D_0=0.17 NN=6 MM=8}The switching functions to use for each of the contacts in your map
hlda:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1.contact-1,d2.contact-1,d3.contact-1,d4.contact-1,d5.contact-1,d6.contact-1the input to this functionCOEFFICIENTS=0.6188,0.5975,0.5045,-0.0708,0.0217,0.0140the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionOPES_METAD...On-the-fly probability enhanced sampling with metadynamics-like target distribution. More detailsLABEL=opesa label for the action so that its output can be referenced in the input to other actionsARG=deepTDA.node-0the input for this action is the scalar output from one or more other actionsFILE=Kernels.dataa file in which the list of all deposited kernels is storedSTATE_RFILE=compressed.Kernelsread from this file the compressed kernels and all the info needed to RESTART the simulationSTATE_WFILE=compressed.Kernelswrite to this file the compressed kernels and all the info needed to RESTART the simulationPACE=500the frequency for kernel depositionTEMP=340temperatureBARRIER=30the free energy barrier to be overcomeRESTART=NO ... OPES_METADallows per-action setting of restart (YES/NO/AUTO)Print quantities to a file. More detailsSTRIDE=100the frequency with which the quantities of interest should be outputARG=hlda,rmsd_ca,deepLDA.node-0,deepTICA.node-0,deepTDA.node-0,opes.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVARbthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities