Project ID: plumID:22.004
Source: input_files/Aldol_reaction/2_Sampling/plumed.dat
Originally used with PLUMED version: 2.8
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.
#UNITSUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
#LOAD FILES (or include them in PLUMED)LOADLoads a library, possibly defining new actions. More detailsFILE=Contacts.cppfile to be loaded
#DEFINE GROUP OF ATOMS C: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=1,4,8 O: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=6,11 H: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=2,3,5,7,9,10the numerical indexes for the set of atoms in the group
#DEFINE CONTACTS cc2:CONTACTSGROUPA=C SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} oo2:This action is not part of PLUMED and was included by using a LOAD command More detailsCONTACTSGROUPA=O SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} co2:This action is not part of PLUMED and was included by using a LOAD command More detailsCONTACTSGROUPA=C GROUPB=O SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} ch2:This action is not part of PLUMED and was included by using a LOAD command More detailsCONTACTSGROUPA=C GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} oh2:This action is not part of PLUMED and was included by using a LOAD command More detailsCONTACTSGROUPA=O GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This action is not part of PLUMED and was included by using a LOAD command More details
#LOAD PYTHORCH MODEL auto:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=model.ptFilename of the PyTorch compiled modelARG=cc2.*,oo2.*,co2.*,ch2.*,oh2 NNcube:the input for this action is the scalar output from one or more other actionsMATHEVALAn alias to the ef CUSTOM function. More detailsARG=auto.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
#DEFINE WALLS WALLS com1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=1-7 com2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=8-11 dc1:the list of atoms which are involved the virtual atom's definitionDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com2the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dc1the arguments on which the bias is actingAT=+5.0the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsLABEL=uwall_1a label for the action so that its output can be referenced in the input to other actions
nnuw:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=NNcubethe arguments on which the bias is actingAT=3.2the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2 nnlw:the powers for the wallsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=NNcubethe arguments on which the bias is actingAT=-3.2the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the walls
#OPES CALCULATIONOPES_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=NNcubethe input for this action is the scalar output from one or more other actionsPACE=500the frequency for kernel depositionBARRIER=160the free energy barrier to be overcomeSIGMA=0.10the initial widths of the kernelsTEMP=300 ... OPES_METADtemperature
#MONITOR DISTANCES c1c8:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,8the pair of atom that we are calculating the distance betweenNOPBCo6h7:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=6,7the pair of atom that we are calculating the distance betweenNOPBCo11h7:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,7the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesPrint quantities to a file. More detailsSTRIDE=20the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesARG=NNcube,opes.*,*.biasthe input for this action is the scalar output from one or more other actions