PLUMED-NEST

Project ID: plumID:19.079
Source: nest/ha_glu/plumed.dat
Originally used with PLUMED version: 2.4.2
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

# vim: ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

# Ref atom on surf
refThe GROUP action with label ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ref
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=2081

# Entire peptide COM to surface
cThe COM action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
atoms
virtual atom calculated by COM action: 
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
=1-27
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d.x
scalar
the x-component of the vector connecting the two atoms
d.y
scalar
the y-component of the vector connecting the two atoms
d.z
scalar
the z-component of the vector connecting the two atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ref,c 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

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
=mtdThe METAD action with label mtd calculates the following quantities:
 Quantity   
 Type   
 Description  
mtd.bias
scalar
the instantaneous value of the bias potential
ARG
the input for this action is the scalar output from one or more other actions
=d.z 
PACE
the frequency for hill addition
=1000
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=0.01
FILE
 a file in which the list of added hills is stored
=HILLS
GRID_MIN
the lower bounds for the grid
=-1
GRID_MAX
the upper bounds for the grid
=10
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD

## wall 
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
=d.z 
AT
the positions of the wall
=3.0 
KAPPA
the force constant for the wall
=50000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

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
=1000 
FILE
the name of the file on which to output these quantities
=COLVAR