Project ID: plumID:19.077
Source: LYS_NNH.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
#RESTART
#CVs 
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
MOLTYPE
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein
STRUCTURE
a file in pdb format containing a reference structure
=lys.pdb c1:
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
=1-34 #COM from peptide to surface d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1945,c1
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances
#dist peptide to surface
#restraint wall1:
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
=d1.z
AT
the positions of the wall
=3.0
KAPPA
the force constant for the wall
=1500
#pb
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
=d1.z
SIGMA
the widths of the Gaussian hills
=0.05
HEIGHT
the heights of the Gaussian hills
=0.2 #kj/mol
PACE
the frequency for hill addition
=500
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
GRID_MIN
the lower bounds for the grid
=-3.0
GRID_MAX
the upper bounds for the grid
=7.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
FILE
a file in which the list of added hills is stored
=HILLS.d1 ... 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
=d1.z,metad.bias
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=COLVAR