Project ID: plumID:21.015
Source: US/CBM5/plumed9.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
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

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
restraint-bnd:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=distx
KAPPA
specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=100.0
AT
the position of the restraint
=2.6
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=distx,restraint-bnd.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
=COLVAR9