PLUMED-NEST

Project ID: plumID:21.004
Source: GSK/3/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

RESTART
Activate restart. More details

The RESTART action with label  calculates something
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
=1-5640 
ENTITY1
the atoms that make up a molecule that you wish to align
=5641-5700 
STRIDE
 the frequency with which molecules are reassembled
=1

pThe PATHMSD action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.sss
scalar
the position on the path
p.zzz
scalar
the distance from the path: 
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
=230.00 
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units
=4 
NEIGH_SIZE
size of the neighbor list
=8

metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential: 
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. 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
=69,0.18
meta: 
METAD
Used to performed metadynamics on one or more collective 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
=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
=69,0.18  
FILE
 a file in which the list of added hills is stored
=HILLS
uwall_zThe UPPER_WALLS action with label uwall_z calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_z.bias
scalar
the instantaneous value of the bias potential
uwall_z.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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
=400000.0
lwall_s_oThe LOWER_WALLS action with label lwall_s_o calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall_s_o.bias
scalar
the instantaneous value of the bias potential
lwall_s_o.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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_iThe UPPER_WALLS action with label uwall_s_i calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_s_i.bias
scalar
the instantaneous value of the bias potential
uwall_s_i.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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
=70 
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