PLUMED-NEST

Project ID: plumID:19.030
Source: plumed_2.dat
Originally used with PLUMED version: 2.5.1
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

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
=1-176
helix1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-88
helix2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=89-176

dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=helix1,helix2

The DISTANCE action with label dist calculates a scalar quantity
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
=dist 
SIGMA
the widths of the Gaussian hills
=0.05 
HEIGHT
the heights of the Gaussian hills
=0.05 
PACE
the frequency for hill addition
=5000 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=323 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
GRID_MIN
the lower bounds for the grid
=-0.5 
GRID_MAX
the upper bounds for the grid
=7.5 
GRID_BIN
the number of bins for the grid
=400 
FILE
 a file in which the list of added hills is stored
=HILLS

The METAD action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the 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
=dist 
AT
the positions of the wall
=4.5 
KAPPA
the force constant for the wall
=3000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall
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
=dist 
AT
the positions of the wall
=0.0 
KAPPA
the force constant for the wall
=3000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall

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
=100 
FILE
the name of the file on which to output these quantities
=COLVAR