PLUMED-NEST-TEST-SITE

Project ID: plumID:21.020
Source: dimer/smd/plumed2.inp
Originally used with PLUMED version: 2.8
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

UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

The UNITS action with label  calculates something
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dist

The DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.value
the DISTANCE between this pair of atoms
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
=dist 
AT
the positions of the wall
=7.0 
KAPPA
the force constant for the wall
=1.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=walls

The UPPER_WALLS action with label walls calculates the following quantities:
 Quantity   
 Description  
walls.bias
the instantaneous value of the bias potential
walls.force2
the instantaneous value of the squared force due to this bias potential
MOVINGRESTRAINT
Add a time-dependent, harmonic restraint on one or more variables. This action has hidden defaults. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=dist
  
STEP0
This keyword appears multiple times as STEPx with x=0,1,2,
=0       
AT0
ATx is equal to the position of the restraint at time STEPx
=0.8  
KAPPA0
KAPPAx is equal to the value of the force constants at time STEPx
=1000.0
  
STEP1
This keyword appears multiple times as STEPx with x=0,1,2,
=500000  
AT1
ATx is equal to the position of the restraint at time STEPx
=8.0  
KAPPA1
KAPPAx is equal to the value of the force constants at time STEPx
=1000.0
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=res
... MOVINGRESTRAINT
The MOVINGRESTRAINT action with label res calculates the following quantities:
 Quantity   
 Description  
res.bias
the instantaneous value of the bias potential
res.work
the total work performed changing this restraint
res.force2
the instantaneous value of the squared force due to this bias potential
res._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
res._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
res._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input file
MOVINGRESTRAINT
Add a time-dependent, harmonic restraint on one or more variables. This action uses the defaults shown here. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=dist
  
STEP0
This keyword appears multiple times as STEPx with x=0,1,2,
=0       
AT0
ATx is equal to the position of the restraint at time STEPx
=0.8  
KAPPA0
KAPPAx is equal to the value of the force constants at time STEPx
=1000.0
  
STEP1
This keyword appears multiple times as STEPx with x=0,1,2,
=500000  
AT1
ATx is equal to the position of the restraint at time STEPx
=8.0  
KAPPA1
KAPPAx is equal to the value of the force constants at time STEPx
=1000.0
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=res
 
VERSE
 Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B)
=B
... MOVINGRESTRAINT

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
=10000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dist,res.work 
STRIDE
 the frequency with which the quantities of interest should be output
=50 
FILE
the name of the file on which to output these quantities
=colvar