PLUMED-NEST

Project ID: plumID:21.004
Source: HST-GST/CB8-G6/plumed_path.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

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RESTART
Activate restart. More details

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
=1-168 
STRIDE
 the frequency with which molecules are reassembled
=1
p: 
PATHMSD
This Colvar calculates path collective variables. More details
 
REFERENCE
the pdb is needed to provide the various milestones
=path.pdb  
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=230.0 
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units
=4 
NEIGH_SIZE
size of the neighbor list
=8

The PATHMSD action with label p calculates the following quantities:
 Quantity   
 Description  
p.sss
the position on the path
p.zzz
the distance from the pathmeta: 
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
=p.sss,p.zzz 
SIGMA
the widths of the Gaussian hills
=0.2,0.01 
HEIGHT
the heights of the Gaussian hills
=0.84 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
PACE
the frequency for hill addition
=500 
GRID_MIN
the lower bounds for the grid
=1,-0.015 
GRID_MAX
the upper bounds for the grid
=55,0.19
The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potentialuwall_z: 
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
=p.zzz 
AT
the positions of the wall
=0.05 
KAPPA
the force constant for the wall
=40000000.0
lwall_s_o: 
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
=p.sss 
AT
the positions of the wall
=1  
KAPPA
the force constant for the wall
=20000.0
uwall_s_i: 
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
=p.sss 
AT
the positions of the wall
=55 
KAPPA
the force constant for the wall
=20000.0

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=p.sss,p.zzz 
STRIDE
 the frequency with which the quantities of interest should be output
=250 
FILE
the name of the file on which to output these quantities
=COLV_Path 
FMT
the format that should be used to output real numbers
=%8.4f