Project ID: plumID:22.029
Source: metad.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 onv2.8
tested onmaster
# RESTART append output files of several restarts
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
=1-85
#groups ang_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_meta2.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=ang_noh waters_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_meta2.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=ang_noh donors:
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_meta2.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=donors acceptors:
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_meta2.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=acceptors #gyration radius
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
TYPE
The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-85
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg
#walls uw:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=rg
KAPPA
the force constant for the wall
=10000
AT
the positions of the wall
=0.85 lw:
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=rg
KAPPA
the force constant for the wall
=10000
AT
the positions of the wall
=0.5
# Coordination number c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=ang_noh
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=waters_noh
R_0
The r_0 parameter of the switching function
=0.35 hbs:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=donors
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=acceptors
R_0
The r_0 parameter of the switching function
=0.25
# Metadynamics
METAD
Used to performed metadynamics on one or more collective variables. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=rg,hbs
GRID_MIN
the lower bounds for the grid
=0,0
GRID_MAX
the upper bounds for the grid
=1,56
SIGMA
the widths of the Gaussian hills
=0.1,0.1
HEIGHT
the heights of the Gaussian hills
=1.2
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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... 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
=rg
FILE
the name of the file on which to output these quantities
=rg.dat
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
=metad
FILE
the name of the file on which to output these quantities
=metad_data.dat
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
=c
FILE
the name of the file on which to output these quantities
=all_coordination_45.dat
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
=hbs
FILE
the name of the file on which to output these quantities
=all_coordination_25.dat
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
=rg,hbs,metad.bias
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
=lw.*,uw
FILE
the name of the file on which to output these quantities
=restraint.dat
STRIDE
the frequency with which the quantities of interest should be output
=500
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