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
tested onv2.9
tested onmaster
tested on master
# vim: ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.

#UNITS
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
#LOAD FILES
LOAD
Loads a library, possibly defining new actions. More details
FILE
file 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:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=10,11
NOPBC
ignore the periodic boundary conditions when calculating distances
d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=11,1
NOPBC
ignore the periodic boundary conditions when calculating distances
d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=10,2
NOPBC
ignore the periodic boundary conditions when calculating distances
d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=11,2
NOPBC
ignore the periodic boundary conditions when calculating distances
d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the 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 H:
GROUP
Define 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
ATOMS
the numerical indexes for the set of atoms in the group
=3,4,6,7,8,9,11 dHH:
DISTANCES
Calculate the distances between multiple piars of atoms More details
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H
MIN
calculate the minimum value
={BETA=20}
NOPBC
ignore the periodic boundary conditions when calculating distances
wallHH:
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=dHH
AT
the positions of the wall
=1.4
KAPPA
the 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 uwall:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=d1,d2,d3,d4,d5
AT
the positions of the wall
=3.0,3.0,3.0,3.0,3.0
KAPPA
the force constant for the wall
=250.0,250.0,250.0,250.0,250.0
# fix hydrogens on C1 -> bonding Br lateral d13:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,3
NOPBC
ignore the periodic boundary conditions when calculating distances
d14:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,4
NOPBC
ignore the periodic boundary conditions when calculating distances
wallCe1H1:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=d13,d14
AT
the positions of the wall
=1.4,1.4
KAPPA
the 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 d57:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=5,7
NOPBC
ignore the periodic boundary conditions when calculating distances
d58:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=5,8
NOPBC
ignore the periodic boundary conditions when calculating distances
d59:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=5,9
NOPBC
ignore the periodic boundary conditions when calculating distances
wallCe2H2:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=d57,d58,d59
AT
the positions of the wall
=1.4,1.4,1.4
KAPPA
the 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 d26:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2,6
NOPBC
ignore the periodic boundary conditions when calculating distances
wallCmH1:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=d26
AT
the positions of the wall
=1.4
KAPPA
the 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 C:
GROUP
Define 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
ATOMS
the numerical indexes for the set of atoms in the group
=1,2,5 #H: GROUP ATOMS=3,4,6,7,8,9,11 Br:
GROUP
Define 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
ATOMS
the numerical indexes for the set of atoms in the group
=10
cc2:
CONTACTS
This 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:
CONTACTS
This 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:
CONTACTS
This 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:
CONTACTS
This 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_MODEL
Load a PyTorch model compiled with TorchScript. More details
FILE
Filename of the PyTorch compiled model
=deepTDA_hBromination_2D.pt
ARG
the input for this action is the scalar output from one or more other actions
=cc2.*,cb2.*,ch2.*,bh2 #nncv: PYTORCH_MODEL2 MODEL=../deepTDA_hBromination_2D.pt ARG=cc2.*,cb2.*,ch2.*,bh2.* # if TorchTestModel.cpp is loaded
# ====== METAD ====== opes:
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=nncv.node-0,nncv.node-1
PACE
the frequency for kernel deposition
=500
BARRIER
the free energy barrier to be overcome
=240
SIGMA
the initial widths of the kernels
=0.20,0.20
TEMP
temperature
=300 ...
# ====== OUTPUT ======
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=distances
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=contacts
ARG
the input for this action is the scalar output from one or more other actions
=cc2.*,cb2.*,ch2.*,bh2
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=colvar
ARG
the input for this action is the scalar output from one or more other actions
=nncv.node-0,nncv.node-1,opes.*,d1,d2,d3,d4,d5,wallHH.*,uwall.*,wallCe1H1.*,wallCe2H2.*,wallCmH1