Project ID: plumID:21.015
Source: MetaD/CBM5/plumed.dat
Originally used with PLUMED version: 2.5
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
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
ENTITY0
the atoms that make up a molecule that you wish to align
=721-887
a1:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=798-801 a2:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=803-807 a3:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=832-835 achi:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-720
p1:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=a1
NOPBC
ignore the periodic boundary conditions when calculating distances
p2:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=a2
NOPBC
ignore the periodic boundary conditions when calculating distances
p3:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=a3
NOPBC
ignore the periodic boundary conditions when calculating distances
pchi:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=achi
NOPBC
ignore the periodic boundary conditions when calculating distances

c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=798-801,803-807,832-835
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=1-720
R_0
The r_0 parameter of the switching function
=0.5
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=0.7
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 distx:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=p1.x,p2.x,p3.x,pchi.x
VAR
the names to give each of the arguments in the function
=a,b,c,y
FUNC
the function you wish to evaluate
=((y-a)^2+(y-b)^2+(y-c)^2)^0.5
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
METAD
Used to performed metadynamics on one or more collective variables. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=c,distx
SIGMA
the widths of the Gaussian hills
=0.5,0.5
HEIGHT
the heights of the Gaussian hills
=2.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
PACE
the frequency for hill addition
=500
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50.0
FILE
a file in which the list of added hills is stored
=HILLS
GRID_MIN
the lower bounds for the grid
=0.0,0.0
GRID_MAX
the upper bounds for the grid
=75.0,35.0
GRID_BIN
the number of bins for the grid
=375,175
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad ... METAD
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=c,distx,metad.bias
STRIDE
the frequency with which the quantities of interest should be output
=5000
FILE
the name of the file on which to output these quantities
=COLVAR