PLUMED-NEST-TEST-SITE

Project ID: plumID:21.028
Source: hBromination/2D_deepTDA/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

Click on the labels of the actions for more information on what each action computes

# 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
The UNITS action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../Contacts.cpp
#LOAD FILE=TorchModelTest.cpp

# Atoms labels: [1-c1][2-c2][3-h1][4-h2][5-c5][6-h3][7-h4][8-h5][9-h6][10-b1][11-h7]

# Traditional distances 
d1:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,11 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,1 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,2 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1 NOPBC ignore the periodic boundary conditions when calculating distances

# ========= walls definition =========
# prevent hydrogen molecules 
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsH: 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=3,4,6,7,8,9,11
The GROUP action with label H calculates somethingdHH: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MINcalculate the minimum value={BETA=20} NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCES action with label dHH calculates the following quantities:
 Quantity   
 Description  
dHH.min
the minimum colvar
dHH.value
the DISTANCES between the each pair of atoms that were specifiedwallHH: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dHH.* ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=250.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1.0 #OFFSET=1.3

# keep COMs near
The LOWER_WALLS action with label wallHH calculates the following quantities:
 Quantity   
 Description  
wallHH.bias
the instantaneous value of the bias potential
wallHH.force2
the instantaneous value of the squared force due to this bias potentialuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4,d5 ATthe positions of the wall=3.0,3.0,3.0,3.0,3.0 KAPPAthe force constant for the wall=250.0,250.0,250.0,250.0,250.0 

# fix hydrogens on C1 -> bonding Br lateral
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentiald13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Description  
d13.value
the DISTANCE between this pair of atomsd14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,4 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Description  
d14.value
the DISTANCE between this pair of atomswallCe1H1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d13,d14 ATthe positions of the wall=1.4,1.4 KAPPAthe force constant for the wall=450.0,450.0 EXP the powers for the walls=2,2 EPS the values for s_i in the expression for a wall=1.0,1.0 OFFSET the offset for the start of the wall=0.2,0.2

# fix hydrogens on C3 -> nonbonding Br lateral
The UPPER_WALLS action with label wallCe1H1 calculates the following quantities:
 Quantity   
 Description  
wallCe1H1.bias
the instantaneous value of the bias potential
wallCe1H1.force2
the instantaneous value of the squared force due to this bias potentiald57: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d57 calculates the following quantities:
 Quantity   
 Description  
d57.value
the DISTANCE between this pair of atomsd58: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,8 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d58 calculates the following quantities:
 Quantity   
 Description  
d58.value
the DISTANCE between this pair of atomsd59: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d59 calculates the following quantities:
 Quantity   
 Description  
d59.value
the DISTANCE between this pair of atomswallCe2H2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d57,d58,d59 ATthe positions of the wall=1.4,1.4,1.4 KAPPAthe force constant for the wall=450.0,450.0,450.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1.0,1.0,1.0 OFFSET the offset for the start of the wall=0.2,0.2,0.2

# fix hydrogen on C2 -> bonding Br central
The UPPER_WALLS action with label wallCe2H2 calculates the following quantities:
 Quantity   
 Description  
wallCe2H2.bias
the instantaneous value of the bias potential
wallCe2H2.force2
the instantaneous value of the squared force due to this bias potentiald26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Description  
d26.value
the DISTANCE between this pair of atomswallCmH1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d26 ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=450.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1.0 OFFSET the offset for the start of the wall=0.2

# ====== CONTACTS =======
#DEFINE GROUP OF ATOMS
The UPPER_WALLS action with label wallCmH1 calculates the following quantities:
 Quantity   
 Description  
wallCmH1.bias
the instantaneous value of the bias potential
wallCmH1.force2
the instantaneous value of the squared force due to this bias potentialC: 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=1,2,5
#H: GROUP ATOMS=3,4,6,7,8,9,11
The GROUP action with label C calculates somethingBr: 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=10

The GROUP action with label Br calculates somethingcc2: 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}
cb2: CONTACTSThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=C GROUPB=Br SWITCH={RATIONAL D_0=0.0 R_0=1.9 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}
bh2: CONTACTSThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=Br GROUPB=H SWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}

nncv: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=deepTDA_hBromination_2D.pt ARGthe labels of the values from which the function is calculated=cc2.*,cb2.*,ch2.*,bh2.*
#nncv: PYTORCH_MODEL2 MODEL=../deepTDA_hBromination_2D.pt ARG=cc2.*,cb2.*,ch2.*,bh2.*   # if TorchTestModel.cpp is loaded

# ====== METAD ======
The PYTORCH_MODEL action with label nncv calculates the following quantities:
 Quantity   
 Description  
nncv.node
Model outputsopes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ...
        ARGthe labels of the scalars on which the bias will act=nncv.node-0,nncv.node-1
        PACEthe frequency for kernel deposition=500
        BARRIERthe free energy barrier to be overcome=240
        SIGMA the initial widths of the kernels=0.20,0.20
        TEMP temperature=300
...

# ====== OUTPUT ======
The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the biasPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=distances ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=contacts ARGthe labels of the values that you would like to print to the file=cc2.*,cb2.*,ch2.*,bh2.*
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 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=nncv.node-0,nncv.node-1,opes.*,d1,d2,d3,d4,d5,wallHH.*,uwall.*,wallCe1H1.*,wallCe2H2.*,wallCmH1.*