Project ID: plumID:20.004
Source: aldol/3_enhanced_sampling/plumed.dat
Originally used with PLUMED version: 2.5-dev
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 FILESLOADLoads 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=../2_training_model/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 quantitiesARGthe input for this action is the scalar output from one or more other actionsFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000the frequency with which all the open files should be flushed