PLUMED-NEST

Project ID: plumID:19.079
Source: nest/tio2_gla/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
ref: 
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
=2574

# Entire peptide COM to surface
c: 
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
=1-29
d: 
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

The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.x
the x-component of the vector connecting the two atoms
d.y
the y-component of the vector connecting the two atoms
d.z
the z-component of the vector connecting the two atoms
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
=mtd
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 
The METAD action with label mtd calculates the following quantities:
 Quantity   
 Description  
mtd.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
=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
=uwall

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