PLUMED-NEST

Project ID: plumID:19.045
Source: Walker_16/plumed.equi.inp
Originally used with PLUMED version: 2.3
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

# Restart command
RESTART
Activate restart. More details

# Units
The RESTART action with label  calculates something
UNITS
This command sets the internal units for the code. More details
 
ENERGY
the units of energy
=eV 
LENGTH
the units of lengths
=A 
TIME
the units of time
=ps

# Water oxygens group
owThe GROUP action with label ow calculates the following quantities:
 Quantity   
 Type   
 Description  
ow
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
=25205-60049:3

# Position of the adsorbate
p1The POSITION action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.x
scalar
the x-component of the atom position
p1.y
scalar
the y-component of the atom position
p1.z
scalar
the z-component of the atom position: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# cation-water coordination no
c1The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=13365 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=ow 
D_0
 The d_0 parameter of the switching function
=2.1 
R_0
The r_0 parameter of the switching function
=1.0 
NN
 The n parameter of the switching function 
=4 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=7 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20

# Walls free energy - position
lwallp1xThe LOWER_WALLS action with label lwallp1x calculates the following quantities:
 Quantity   
 Type   
 Description  
lwallp1x.bias
scalar
the instantaneous value of the bias potential
lwallp1x.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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
=p1.x 
AT
the positions of the wall
=53.0 
KAPPA
the force constant for the wall
=1  
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
uwallp1xThe UPPER_WALLS action with label uwallp1x calculates the following quantities:
 Quantity   
 Type   
 Description  
uwallp1x.bias
scalar
the instantaneous value of the bias potential
uwallp1x.force2
scalar
the instantaneous value of the squared force due to this 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
=p1.x 
AT
the positions of the wall
=72.0 
KAPPA
the force constant for the wall
=1  
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
lwallp1yThe LOWER_WALLS action with label lwallp1y calculates the following quantities:
 Quantity   
 Type   
 Description  
lwallp1y.bias
scalar
the instantaneous value of the bias potential
lwallp1y.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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
=p1.y 
AT
the positions of the wall
=32.5 
KAPPA
the force constant for the wall
=1  
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
uwallp1yThe UPPER_WALLS action with label uwallp1y calculates the following quantities:
 Quantity   
 Type   
 Description  
uwallp1y.bias
scalar
the instantaneous value of the bias potential
uwallp1y.force2
scalar
the instantaneous value of the squared force due to this 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
=p1.y 
AT
the positions of the wall
=39.0 
KAPPA
the force constant for the wall
=1  
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
uwallp1zThe UPPER_WALLS action with label uwallp1z calculates the following quantities:
 Quantity   
 Type   
 Description  
uwallp1z.bias
scalar
the instantaneous value of the bias potential
uwallp1z.force2
scalar
the instantaneous value of the squared force due to this 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
=p1.z 
AT
the positions of the wall
=50.0 
KAPPA
the force constant for the wall
=1  
EXP
 the powers for the walls
=4 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0

# Metadynamics
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. 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
=p1.x,p1.z,c1
  
SIGMA
the widths of the Gaussian hills
=0.2,0.2,0.2
  
PACE
the frequency for hill addition
=1000000
  
HEIGHT
the heights of the Gaussian hills
=0.026
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
  
WALKERS_DIR
shared directory with the hills files from all the walkers
=../HILLS_DIR 
WALKERS_RSTRIDE
stride for reading hills files
=500 
WALKERS_N
number of walkers
=30 
WALKERS_ID
walker id
=16
... METAD
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. 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
=p1.x,p1.z,c1
  
SIGMA
the widths of the Gaussian hills
=0.2,0.2,0.2
  
PACE
the frequency for hill addition
=1000000
  
HEIGHT
the heights of the Gaussian hills
=0.026
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
  
WALKERS_DIR
shared directory with the hills files from all the walkers
=../HILLS_DIR 
WALKERS_RSTRIDE
stride for reading hills files
=500 
WALKERS_N
number of walkers
=30 
WALKERS_ID
walker id
=16
 
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD

# Print CV
PRINT
Print quantities to a file. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=p1.x,p1.y,p1.z,c1,lwallp1x.bias,uwallp1x.bias,lwallp1y.bias,uwallp1y.bias,uwallp1z.bias
  
FILE
the name of the file on which to output these quantities
=COLVAR 
  
STRIDE
 the frequency with which the quantities of interest should be output
=1000
... PRINT
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1000