PLUMED-NEST

Project ID: plumID:23.013
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

#RESTART
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=nm 
TIME
the units of time
=ps 
ENERGY
the units of energy
=kj/mol
TIME
retrieve the time of the simulation to be used elsewhere More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=tim
The TIME action with label tim calculates a scalar quantity
PATHMSD
This Colvar calculates path collective variables. More details
 
REFERENCE
the pdb is needed to provide the various milestones
=sting-traj-based-path-CA+MET-SD.pdb 
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=1158 
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 
FULLSAMPLES
 number of samples in a bin prior to application of the ABF
=2000 
GRID_MIN
the lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=1 
GRID_MAX
the upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=32 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.05 
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 
TAU
 specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars
=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
=250000 
HISTORYFREQ
save history to a file every N steps
=2500000 
DRR_RFILE
specifies the restart file (
=drr 
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 
SIGMA
the widths of the Gaussian hills
=0.25 
HEIGHT
the heights of the Gaussian hills
=1.8 
PACE
the frequency for hill addition
=500 
GRID_MIN
the lower bounds for the grid
=0 
GRID_MAX
the upper bounds for the grid
=33 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.05 
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
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((200-x)*0.1)+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
=stp1
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((x-200)*0.1)+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
=stp2
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((300-x)*0.1)+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
=stp3
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((x-300)*0.1)+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
=stp4
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((400-x)*0.1)+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
=stp5
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((x-400)*0.1)+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
=stp6
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((500-x)*0.1)+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
=stp7
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=tim 
FUNC
the function you wish to evaluate
=0.5*(erf((x-500)*0.1)+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
=stp8
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=stp1,stp2,stp3,stp4,stp5,stp6,stp7,stp8 
VAR
the names to give each of the arguments in the function
=x1,x2,x3,x4,x5,x6,x7,x8 
FUNC
the function you wish to evaluate
=0.15*x1+0.125*x2*x3+0.1*x4*x5+0.075*x6*x7+0.05*x8 
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
=max_z
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=path_z,max_z 
FUNC
the function you wish to evaluate
=(y-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
=uwz_arg
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
=uwz_arg 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uw_path_z
The BIASVALUE action with label uw_path_z calculates the following quantities:
 Quantity   
 Description  
uw_path_z.bias
the instantaneous value of the bias potential
uw_path_z._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
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
=32 
KAPPA
the force constant for the wall
=1000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uw_s
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
=1  
KAPPA
the force constant for the wall
=1000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lw_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
=drr.path.sss_fict 
AT
the positions of the wall
=32 
KAPPA
the force constant for the wall
=1000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uw_s_fict
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
=drr.path.sss_fict 
AT
the positions of the wall
=1  
KAPPA
the force constant for the wall
=1000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lw_s_fict
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-force.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