PLUMED-NEST

Project ID: plumID:22.001
Source: lammps/CaCO3/metad/plumed.1.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 NATOMS=100000
# 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. 
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
dist:  
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

The DISTANCE action with label dist calculates a scalar quantity
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
=coord
  
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
The COORDINATION action with label coord calculates a scalar quantity
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
=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
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 input for this action is the scalar output from one or more other actions
=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
=wall
... UPPER_WALLS
# --- End of included input --- 
The UPPER_WALLS action with label wall calculates the following quantities:
 Quantity   
 Description  
wall.bias
the instantaneous value of the bias potential
wall.force2
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
=100 
FILE
the name of the file on which to output these quantities
=COLVAR