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.
#UNITS UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A #LOAD FILES (or include them in PLUMED) LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=Contacts.cpp #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 details ATOMSthe numerical indexes for the set of atoms in the group=1,4,8 O: 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=6,11 H: 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=2,3,5,7,9,10 #DEFINE CONTACTS cc2: CONTACTSThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=C SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} oo2: CONTACTSThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=O SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} co2: CONTACTSThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=C GROUPB=O SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} ch2: CONTACTSThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=C GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} oh2: CONTACTSThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=O GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
#LOAD PYTHORCH MODEL auto: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=model.pt ARGthe labels of the values from which the function is calculated=cc2.*,oo2.*,co2.*,ch2.*,oh2.* NNcube: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=auto.node-0 FUNCthe function you wish to evaluate=x+x^3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO #DEFINE WALLS WALLS com1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-7 com2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=8-11 dc1: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=com1,com2 NOPBC ignore the periodic boundary conditions when calculating distances UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dc1 ATthe positions of the wall=+5.0 KAPPAthe force constant for the wall=150.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_1
nnuw: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=NNcube ATthe positions of the wall=3.2 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 nnlw: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=NNcube ATthe positions of the wall=-3.2 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 #OPES CALCULATION 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=NNcube PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=160 SIGMA the initial widths of the kernels=0.10 TEMP temperature=300 ... OPES_METAD
#MONITOR DISTANCES c1c8: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,8 NOPBC ignore the periodic boundary conditions when calculating distances o6h7: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,7 NOPBC ignore the periodic boundary conditions when calculating distances o11h7: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,7 NOPBC ignore the periodic boundary conditions when calculating distances
#PRINT PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=20 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=NNcube,opes.*,*.bias