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

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 (or include them in PLUMED)
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=Contacts.cpp
#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
=1,4,8 O:
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
=6,11 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
=2,3,5,7,9,10
#DEFINE CONTACTS 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} oo2:
CONTACTS
This 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:
CONTACTS
This 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:
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} oh2:
CONTACTS
This 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_MODEL
Load a PyTorch model compiled with TorchScript. More details
FILE
Filename of the PyTorch compiled model
=model.pt
ARG
the input for this action is the scalar output from one or more other actions
=cc2.*,oo2.*,co2.*,ch2.*,oh2 NNcube:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=auto.node-0
FUNC
the function you wish to evaluate
=x+x^3
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
#DEFINE WALLS WALLS com1:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-7 com2:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=8-11 dc1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=com1,com2
NOPBC
ignore the periodic boundary conditions when calculating distances
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
=dc1
AT
the positions of the wall
=+5.0
KAPPA
the force constant for the wall
=150.0
EXP
the powers for the walls
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_1
nnuw:
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
=NNcube
AT
the positions of the wall
=3.2
KAPPA
the force constant for the wall
=2000.0
EXP
the powers for the walls
=2 nnlw:
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
=NNcube
AT
the positions of the wall
=-3.2
KAPPA
the force constant for the wall
=2000.0
EXP
the powers for the walls
=2
#OPES CALCULATION
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opes
ARG
the input for this action is the scalar output from one or more other actions
=NNcube
PACE
the frequency for kernel deposition
=500
BARRIER
the free energy barrier to be overcome
=160
SIGMA
the initial widths of the kernels
=0.10
TEMP
temperature
=300 ... OPES_METAD
#MONITOR DISTANCES c1c8:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,8
NOPBC
ignore the periodic boundary conditions when calculating distances
o6h7:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=6,7
NOPBC
ignore the periodic boundary conditions when calculating distances
o11h7:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=11,7
NOPBC
ignore the periodic boundary conditions when calculating distances

#PRINT
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=20
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
=NNcube,opes.*,*.bias