**Project ID:** plumID:21.028

**Source:** benzoquinone_PT/2_biased/plumed.dat

**Originally used with PLUMED version:** 2.7

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

#! vim:ft=plumed

# input file for biased intramolecular double proton transfer in 2,5-diamino-1,4-benzoquinone with Deep-TDA

# we can use the coordination number of the heavy atoms! # we would like to preserve the symmetries

#UNITSUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths

# ==== GROUPS ====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=1,2,3,4,5,6the numerical indexes for the set of atoms in the groupN: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=9,12the numerical indexes for the set of atoms in the groupO: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=15,16the numerical indexes for the set of atoms in the groupH:ATOMS=7,8,10,11,13,14the numerical indexes for the set of atoms in the group

# ==== HEAVY ATOMS ====C1:ATOMS=1the numerical indexes for the set of atoms in the groupC2:ATOMS=2the numerical indexes for the set of atoms in the groupC3:ATOMS=3the numerical indexes for the set of atoms in the groupC4:ATOMS=4the numerical indexes for the set of atoms in the groupC5:ATOMS=5the numerical indexes for the set of atoms in the groupC6:ATOMS=6the numerical indexes for the set of atoms in the groupN1:ATOMS=9the numerical indexes for the set of atoms in the groupN2:ATOMS=12the numerical indexes for the set of atoms in the groupO1:ATOMS=15the numerical indexes for the set of atoms in the groupO2:ATOMS=16the numerical indexes for the set of atoms in the groupc1c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)CSWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCignore the periodic boundary conditions when calculating distancesc1n:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)NSWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCignore the periodic boundary conditions when calculating distancesc1o:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)OSWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCignore the periodic boundary conditions when calculating distancesc1h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distancesc2c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)CNOPBCignore the periodic boundary conditions when calculating distancesc2n:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)NNOPBCignore the periodic boundary conditions when calculating distancesc2o:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)ONOPBCignore the periodic boundary conditions when calculating distancesc2h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distancesc3c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC3GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)CNOPBCignore the periodic boundary conditions when calculating distancesc3n:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC3GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)NNOPBCignore the periodic boundary conditions when calculating distancesc3o:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC3GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)ONOPBCignore the periodic boundary conditions when calculating distancesc3h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC3GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distancesc4c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC4GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)CNOPBCignore the periodic boundary conditions when calculating distancesc4n:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC4GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)NNOPBCignore the periodic boundary conditions when calculating distancesc4o:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC4GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)ONOPBCignore the periodic boundary conditions when calculating distancesc4h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC4GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distancesc5c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)CNOPBCignore the periodic boundary conditions when calculating distancesc5n:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)NNOPBCignore the periodic boundary conditions when calculating distancesc5o:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)ONOPBCignore the periodic boundary conditions when calculating distancesc5h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distancesc6c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC6GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)CNOPBCignore the periodic boundary conditions when calculating distancesc6n:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC6GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)NNOPBCignore the periodic boundary conditions when calculating distancesc6o:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC6GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)ONOPBCignore the periodic boundary conditions when calculating distancesc6h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsC6GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distancesn1h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsN1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distancesn2h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsN2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distanceso1h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsO1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distanceso2h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsO2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)HNOPBCignore the periodic boundary conditions when calculating distances

# ==== PYTORCH MODEL ====nncv:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=deepTDA_benzo.ptFilename of the PyTorch compiled modelARG=the input for this action is the scalar output from one or more other actionsn1h,n2h,o1h,o2h,c1c,c1n,c1o,c1h,c2c,c2n,c2o,c2h,c3c,c3n,c3o,c3h,c4c,c4n,c4o,c4h,c5c,c5n,c5o,c5h,c6c,c6n,c6o,c6h

# ==== LIMIT CV ====lwall_nncv:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingnncv.node-0AT=-16the positions of the wallKAPPA=400the force constant for the walluwall_nncv:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingnncv.node-0AT=+16the positions of the wallKAPPA=400the force constant for the wall

# ==== OPES PARAMETERS ====opes:OPES_METAD...On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More detailsARG=the input for this action is the scalar output from one or more other actionsnncv.node-0PACE=500the frequency for kernel depositionBARRIER=120the free energy barrier to be overcomeSIGMA=0.20the initial widths of the kernelsTEMP=300 ...temperature

# ==== PRINT STUFF ====Print quantities to a file. More detailsFILE=colvarthe name of the file on which to output these quantitiesARG=the input for this action is the scalar output from one or more other actionsnncv.node-0,opes.*,n1h,n2h,o1h,o2h,lwall_nncv.*,uwall_nncvSTRIDE=500the frequency with which the quantities of interest should be output