Project ID: plumID:20.006
Source: metad_GCGR/plumed.dat
Originally used with PLUMED version: 2.4.3
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
#RESTART

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=nowat.pdb

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
=1-471 
ENTITY1
the atoms that make up a molecule that you wish to align
=472-6973 
STRIDE
 the frequency with which molecules are reassembled
=1

open: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=model.TM.open.skipped.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
closed: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=model.TM.closed.skipped.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details


COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=prog
  
ARG
the input to this function
=open,closed
  
COEFFICIENTS
 the coefficients of the arguments in your function
=1,-1
  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dist
  
ARG
the input to this function
=open,closed
  
COEFFICIENTS
 the coefficients of the arguments in your function
=1,1
  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wte
  
ARG
the input for this action is the scalar output from one or more other actions
=ene
  
PACE
the frequency for hill addition
=500000000 # 10us
  
HEIGHT
the heights of the Gaussian hills
=5 
SIGMA
the widths of the Gaussian hills
=1000
  
FILE
 a file in which the list of added hills is stored
=HILLS_WTE.0
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
  
GRID_MIN
the lower bounds for the grid
=-1500000 
GRID_MAX
the upper bounds for the grid
=-500000 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=10
... METAD

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=meta
  
ARG
the input for this action is the scalar output from one or more other actions
=prog,dist
  
SIGMA
the widths of the Gaussian hills
=0.05,0.05 
HEIGHT
the heights of the Gaussian hills
=1.5 
PACE
the frequency for hill addition
=500
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
  
GRID_MIN
the lower bounds for the grid
=-1.2,0.5 
GRID_MAX
the upper bounds for the grid
=1.2,2.0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.005,0.005
  
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD


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
=open,closed,dist 
AT
the positions of the wall
=1.2,1.2,1.6 
KAPPA
the force constant for the wall
=3000.0,3000.0,3000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall


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
=500 
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