PLUMED-NEST

Project ID: plumID:22.001
Source: lammps/CaCO3/metad/plumed.0.dat
Originally used with PLUMED version: 2.8
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

#SETTINGS NREPLICAS=2
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=plumed-common.dat
# The command:
# INCLUDE FILE=plumed-common.dat
# ensures PLUMED loads the contents of the file called plumed-common.dat
# The contents of this file are shown below (click the red comment to hide them).
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
The INCLUDE action with label plumed-common.dat calculates something
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
ENERGY
the units of energy
=eV 
TIME
the units of time
=ps

# CVs
The UNITS action with label  calculates somethingdistThe DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Type   
 Description  
dist
scalar
the DISTANCE between this pair of atoms:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7345,7346

COORDINATION
Calculate coordination numbers. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=coordThe COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Type   
 Description  
coord
scalar
the value of the coordination
  
GROUPA
First list of atoms
=7345
  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=2-7343:3
  
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=1.0 D_0=2.1 NN=4 MM=8}
  
NLIST
 Use a neighbor list to speed up the calculation
  
NL_CUTOFF
The cutoff for the neighbor list
=10
  
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=10
... COORDINATION


# metad with multiple walkers
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
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
  
ARG
the labels of the scalars on which the bias will act
=dist,coord
  
SIGMA
the widths of the Gaussian hills
=0.2,0.1
  
HEIGHT
the heights of the Gaussian hills
=0.025852
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5
  
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
  
PACE
the frequency for hill addition
=1000
  
GRID_MIN
the lower bounds for the grid
=2,3
  
GRID_MAX
the upper bounds for the grid
=13,10
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD

# walls to stay close to associated state
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
=12
  
KAPPA
the force constant for the wall
=12.0
  
EXP
 the powers for the walls
=2
  
EPS
 the values for s_i in the expression for a wall
=1
  
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
=wallThe UPPER_WALLS action with label wall calculates the following quantities:
 Quantity   
 Type   
 Description  
wall.bias
scalar
the instantaneous value of the bias potential
wall.force2
scalar
the instantaneous value of the squared force due to this bias potential
... UPPER_WALLS
# --- End of included input --- 
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
 
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