Project ID: plumID:23.014
Source: CCR5_dimer/plumed_CCR5_dimer.dat
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
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
STRIDE
the frequency with which molecules are reassembled
=1
ENTITY0
the atoms that make up a molecule that you wish to align
=93,169,170,257,259,260,264,268,355,446,557,559,563,653,662,616,30,154,199,333,418,618
ENTITY1
the atoms that make up a molecule that you wish to align
=790,866,867,954,956,957,961,965,1052,1143,1254,1256,1260,1350,1359,769,812,943,992,1162,1210,993
comA:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=616,618 comB:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=30,154,199,333,418,563,618 comC:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=769,812,943,992,1162,1210,1350 comD:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=992,993 com1:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=93,169,170,257,259,260,264,268,355,446,557,559,563,653,662 com2:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=790,866,867,954,956,957,961,965,1052,1143,1254,1256,1260,1350,1359 d:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=com1,com2
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
dd:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d.x,d.y
POWERS
the powers to which you are raising each of the arguments in your function
=2,2
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=dd
POWERS
the powers to which you are raising each of the arguments in your function
=0.5
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO torsion:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=comA,comB,comC,comD
m:
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
=d2,torsion
SIGMA
the widths of the Gaussian hills
=0.04,0.06
HEIGHT
the heights of the Gaussian hills
=0.5
PACE
the frequency for hill addition
=5000
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
GRID_MIN
the lower bounds for the grid
=1.3,-pi
GRID_MAX
the upper bounds for the grid
=8.5,pi
GRID_WFILE
the file on which to write the grid
=GRID_W.dat
GRID_WSTRIDE
write the grid to a file every N steps
=1000000
WALKERS_MPI
Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR

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
=d2
AT
the positions of the wall
=8.0
KAPPA
the force constant for the wall
=5000000.0
EXP
the powers for the walls
=2.0
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
=uwalli
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=d2,torsion
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
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
=1000000