Project ID: plumID:20.025
Source: OAH_G1/plumed.dat
Originally used with PLUMED version: 2.5
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
# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---

HOST:
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
=16-199 #host atoms LIGC:
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
=1-6 #carbon atoms in the ligand l1:
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 #ligand selected atoms l2:
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 l3:
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
=4 l4:
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 WO:
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
=209-6508:3 #water oxygen atoms
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
ENTITY0
the atoms that make up a molecule that you wish to align
=HOST
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
STRIDE
the frequency with which molecules are reassembled
=1
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=conf_template.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL #coordinates alignment lig:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=LIGC
v1:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,2.0 #virtual atoms v2:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,2.25 v3:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,2.5 v4:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,2.75 v5:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,3.0 v6:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,3.25 v7:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,3.5 v8:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.0136,2.0136,3.75
cyl:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=v1,lig
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
radius:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=cyl.x,cyl.y
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- (2) DESCRIPTORS ---
L1:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=l1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 L2:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=l2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 L3:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=l3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 L4:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=l4
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V1:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V2:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V3:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V4:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v4
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V5:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v5
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V6:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v6
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V7:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v7
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 V8:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=v8
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.0
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
d1:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=L1
FUNC
the function you wish to evaluate
=(x/2.5)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO #normalized descriptors d2:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=L2
FUNC
the function you wish to evaluate
=(x/2.5)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d3:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=L3
FUNC
the function you wish to evaluate
=(x/2.5)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d4:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=L4
FUNC
the function you wish to evaluate
=(x/2.5)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d5:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V1
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d6:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V2
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d7:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V3
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d8:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V4
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d9:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V5
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d10:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V6
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d11:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V7
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d12:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=V8
FUNC
the function you wish to evaluate
=(x/2.8)-1.0
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- (3) DEEP-LDA CV and other quantities ---
s:
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
FILE
Filename of the PyTorch compiled model
=modelG1_OAH_a.pt
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 #NN output sw:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=s.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 #Deep-LDA CV
funnel:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=radius,cyl.z
VAR
the names to give each of the arguments in the function
=r,z
FUNC
the function you wish to evaluate
=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
AT
the positions of the wall
=0
ARG
the arguments on which the bias is acting
=funnel
KAPPA
the force constant for the wall
=2000.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=funnelwall #funnel restraint
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
AT
the positions of the wall
=1.8
ARG
the arguments on which the bias is acting
=cyl.z
KAPPA
the force constant for the wall
=4000.0
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
=upper_wall #upper limit of cyl.z
ang:
ANGLE
Calculate an angle. More details
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=v3,v5,8,6 #angle of a ligand's axis with z cosang:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=ang
FUNC
the function you wish to evaluate
=cos(x
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
ene:
ENERGY
Calculate the total potential energy of the simulation box. More details

# --- (4) OPES ---
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
=cyl.z,sw
BARRIER
the free energy barrier to be overcome
=50
PACE
the frequency for kernel deposition
=500
FILE
a file in which the list of all deposited kernels is stored
=../Kernels.data
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=../compressed_Kernels.data
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=../compressed_Kernels.data
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=50000
WALKERS_MPI
switch on MPI version of multiple walkers
... OPES_METAD
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
STRIDE
the frequency with which the quantities of interest should be output
=250
FILE
the name of the file on which to output these quantities
=COLVAR
FMT
the format that should be used to output real numbers
=%8.4f
ENDPLUMED
Terminate plumed input. More details