PLUMED-NEST

Project ID: plumID:23.012
Source: plumed.dat
Originally used with PLUMED version: 2.8.1
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

PATHMSD
This Colvar calculates path collective variables. More details
 
REFERENCE
the pdb is needed to provide the various milestones
=path-CV-equidistant-mcnally.pdb 
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=51250 
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units
=4 
NEIGH_SIZE
size of the neighbor list
=8 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=path
The PATHMSD action with label path calculates the following quantities:
 Quantity   
 Description  
path.sss
the position on the path
path.zzz
the distance from the path
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=path.zzz 
FUNC
the function you wish to evaluate
=sqrt(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=path_z
DRR
Used to performed extended-system adaptive biasing force(eABF) More details
 
ARG
the input for this action is the scalar output from one or more other actions
=path.sss,path_z 
KAPPA
specifies that the restraint is harmonic and what the values of the force constants on each of the variables are (default to $k_BT$/(GRID_SPACING)^2)
=250,2.5e6 
FULLSAMPLES
 number of samples in a bin prior to application of the ABF
=500 
GRID_MIN
the lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=2,0.0 
GRID_MAX
the upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=27,0.045 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.1,0.001 
TEMP
the system temperature - needed when FRICTION is present
=310 
FRICTION
 add a friction to the variable, similar to extended Langevin Damping in Colvars
=8.0,8.0 
TAU
 specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars
=0.5,0.5 
TEXTOUTPUT
 use text output for grad and count files instead of boost::serialization binary output
 
OUTPUTFREQ
write results to a file every N steps
=100000 
HISTORYFREQ
save history to a file every N steps
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=drr
The DRR action with label drr calculates the following quantities:
 Quantity   
 Description  
drr.bias
the instantaneous value of the bias potential
drr._fict
one or multiple instances of this quantity can be referenced elsewhere in the input file
drr._vfict
one or multiple instances of this quantity can be referenced elsewhere in the input file
drr._biasforce
The bias force from eABF/DRR of the fictitious particle
drr._springforce
Spring force between real CVs and extended CVs
drr._fictNoPBC
the positions of fictitious particles (without PBC)
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
=drr.path.sss_fict,drr.path_z_fict 
SIGMA
the widths of the Gaussian hills
=0.5,0.005 
HEIGHT
the heights of the Gaussian hills
=1.5 
PACE
the frequency for hill addition
=500 
GRID_MIN
the lower bounds for the grid
=0,-0.02 
GRID_MAX
the upper bounds for the grid
=29,0.06 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.1,0.001 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310 
FILE
 a file in which the list of added hills is stored
=HILLS 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=path_z 
FUNC
the function you wish to evaluate
=(0.05-x)^-1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=custom_z
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=custom_z 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=z_wall
The BIASVALUE action with label z_wall calculates the following quantities:
 Quantity   
 Description  
z_wall.bias
the instantaneous value of the bias potential
z_wall._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
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
=path.sss 
AT
the positions of the wall
=3 
OFFSET
 the offset for the start of the wall
=0.0 
KAPPA
the force constant for the wall
=100 
EPS
 the values for s_i in the expression for a wall
=1.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_s
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
=path.sss 
AT
the positions of the wall
=26 
OFFSET
 the offset for the start of the wall
=0.0 
KAPPA
the force constant for the wall
=100 
EPS
 the values for s_i in the expression for a wall
=1.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_s
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
=1000 
FILE
the name of the file on which to output these quantities
=plumed-force2.log 
FMT
the format that should be used to output real numbers
=%12.4f
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
=1000