Project ID: plumID:19.045
Source: Walker_14/plumed.mtd.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
tested onv2.9
tested onmaster
# Restart command
RESTART
Activate restart. More details

# Units
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 ow:
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 p1:
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 c1:
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 lwallp1x:
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
=10
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 uwallp1x:
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
=10
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 lwallp1y:
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
=10
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 uwallp1y:
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
=10
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 uwallp1z:
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
=10
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. 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
=1000
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
=14 ... 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