PLUMED-NEST

Project ID: plumID:23.030
Source: T4L_benzene/opes_flooding/template_barr30/plumed.dat
Originally used with PLUMED version: 2.9
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

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
=1-2593 
ENTITY1
the atoms that make up a molecule that you wish to align
=2594-2605
The WHOLEMOLECULES action with label  calculates something
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=heavy_atoms.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

# Group definition
prot_noh: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H
The GROUP action with label prot_noh calculates somethingsph: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=sphere
The GROUP action with label sph calculates somethingbnz: 
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
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=BNZ_noH

The GROUP action with label bnz calculates something
WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
 
ATOMS
wrapped atoms
=bnz 
AROUND
reference atoms
=sph

sph_center: 
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
=sph
The COM action with label sph_center calculates somethingbnz_center: 
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
=bnz

The COM action with label bnz_center calculates somethingsph_coord: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=sph_center 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The POSITION action with label sph_coord calculates the following quantities:
 Quantity   
 Description  
sph_coord.x
the x-component of the atom position
sph_coord.y
the y-component of the atom position
sph_coord.z
the z-component of the atom positionbnz_coord: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=bnz_center 
NOPBC
 ignore the periodic boundary conditions when calculating distances

The POSITION action with label bnz_coord calculates the following quantities:
 Quantity   
 Description  
bnz_coord.x
the x-component of the atom position
bnz_coord.y
the y-component of the atom position
bnz_coord.z
the z-component of the atom positionabs_x: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=bnz_coord.x,sph_coord.x 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label abs_x calculates somethingabs_y: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=bnz_coord.y,sph_coord.y 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label abs_y calculates somethingabs_z: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=bnz_coord.z,sph_coord.z 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The MATHEVAL action with label abs_z calculates somethingrho: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs_x,abs_y,abs_z 
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y+z*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label rho calculates somethingtheta: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs_z,rho 
FUNC
the function you wish to evaluate
=acos(x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=0.,pi
The MATHEVAL action with label theta calculates somethingphi: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=abs_x,abs_y 
FUNC
the function you wish to evaluate
=atan2(y,x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-pi,pi


# Coordination number
The MATHEVAL action with label phi calculates somethingc: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=bnz 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=prot_noh 
R_0
The r_0 parameter of the switching function
=0.45


#OPES Flooding
The COORDINATION action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the value of the coordinationtarget: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=rho 
FUNC
the function you wish to evaluate
=step(x-0.9 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The CUSTOM action with label target calculates somethingopes: 
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
=rho,c
  
PACE
the frequency for kernel deposition
=500
  
BARRIER
the free energy barrier to be overcome
=30
  
TEMP
 temperature
=300.0
  
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=target
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
...

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 bias
COMMITTOR
Does a committor analysis. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=rho
  
STRIDE
 the frequency with which the CVs are analyzed
=1000
  
BASIN_LL1
List of lower limits for basin #
=2.5
  
BASIN_UL1
List of upper limits for basin #
=10.0
... COMMITTOR



PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rho,theta,phi,c,opes 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=opes.bias 
FILE
the name of the file on which to output these quantities
=COLVARb 
STRIDE
 the frequency with which the quantities of interest should be output
=10


FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=500