Project ID: plumID:21.026
Source: plumed_input/plumed.dat
Originally used with PLUMED version: 2.4
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
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
ENERGY
the units of energy
=kcal/mol
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
=1-5946
dist:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1614,5843 dist2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2838,3207 dist3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=473,5093 dist4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=473,5843 #between Lys(N+)374 and com of ASP21 ASP65
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
=351,1038
LABEL
a label for the action so that its output can be referenced in the input to other actions
=coo dist5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=5767,coo
path1:
PATHMSD
This Colvar calculates path collective variables. More details
REFERENCE
the pdb is needed to provide the various milestones
=reference_path-renumb.pdb
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=1.46
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units
=100
NEIGH_SIZE
size of the neighbor list
=20
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
=path1.sss,path1.zzz
PACE
the frequency for hill addition
=400
HEIGHT
the heights of the Gaussian hills
=0.1
SIGMA
the widths of the Gaussian hills
=1,0.15
FILE
a file in which the list of added hills is stored
=HILLS
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
GRID_MIN
the lower bounds for the grid
=-10,-5
GRID_MAX
the upper bounds for the grid
=100,15 ... METAD
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
=path1.zzz
AT
the positions of the wall
=9.0
KAPPA
the force constant for the wall
=100
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=200
ARG
the input for this action is the scalar output from one or more other actions
FILE
the name of the file on which to output these quantities
=COLVAR