PLUMED-NEST

Project ID: plumID:23.019
Source: plm_path_sketchmap/path/plumed.dat
Originally used with PLUMED version: 2.7.2
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

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
=1-6304 # plm5
	
ENTITY1
the atoms that make up a molecule that you wish to align
=6305-6353 # lig
... WHOLEMOLECULES

PATHMSD
This Colvar calculates path collective variables. More details
 ...
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=p1
	
REFERENCE
the pdb is needed to provide the various milestones
=path_15f.pdb
	
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=961 # lambda=2.3/(average_RMSD_between_frames)**2    2.3/0.048907^2
	
NEIGH_SIZE
size of the neighbor list
=5
... PATHMSD

The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.sss
the position on the path
p1.zzz
the distance from the path
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
	
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
	
ARG
the input for this action is the scalar output from one or more other actions
=p1.sss,p1.zzz
	
SIGMA
the widths of the Gaussian hills
=0.1,0.001
	
HEIGHT
the heights of the Gaussian hills
=3.0
	
PACE
the frequency for hill addition
=500
	
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298
	
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
	
GRID_MIN
the lower bounds for the grid
=-1,-0.1
	
GRID_MAX
the upper bounds for the grid
=16,0.2
	
GRID_BIN
the number of bins for the grid
=400,800
	
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
	
FMT
specify format for HILLS files (useful for decrease the number of digits in regtests)
=%8.4f
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
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
=p1.zzz 
AT
the positions of the wall
=0.05 
KAPPA
the force constant for the wall
=50000 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=p1-zzz_uwall

PRINT
Print quantities to a file. More details
 ...
	
STRIDE
 the frequency with which the quantities of interest should be output
=25
	
ARG
the input for this action is the scalar output from one or more other actions
	
FILE
the name of the file on which to output these quantities
=COLVAR
	
FMT
the format that should be used to output real numbers
=%8.4f
... PRINT