Project ID: plumID:19.020
Source: step-2/plumed.1.dat
Originally used with PLUMED version: 2.2
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
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
STRUCTURE
a file in pdb format containing a reference structure
=reference.pdb
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
=1-427
a:
ALPHARMSD
Probe the alpha helical content of a protein structure. More details
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=all
TYPE
the manner in which RMSD alignment is performed
=DRMSD
R_0
The r_0 parameter of the switching function
=0.08
NN
The n parameter of the switching function
=8
MM
The m parameter of the switching function
=12 g:
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
TYPE
The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=9,23,35,50,62,78,89,101,120,135,159,183,202,212,229,253,272,282,297,321,345,362,377,389,400,410 ene:
ENERGY
Calculate the total potential energy of the simulation box. More details

wte:
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
=ene
PACE
the frequency for hill addition
=999999999
HEIGHT
the heights of the Gaussian hills
=2.5
SIGMA
the widths of the Gaussian hills
=500.0
FILE
a file in which the list of added hills is stored
=HILLS_PTWTE
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
=310.799
metad:
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
=a,g
PACE
the frequency for hill addition
=500
HEIGHT
the heights of the Gaussian hills
=0.4184
SIGMA
the widths of the Gaussian hills
=0.15,0.025
FILE
a file in which the list of added hills is stored
=HILLS_PTMetaDWTE
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.799
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=a,g,ene,wte.bias,metad.bias
STRIDE
the frequency with which the quantities of interest should be output
=50
FILE
the name of the file on which to output these quantities
=COLVAR_MetadWTE
ENDPLUMED
Terminate plumed input. More details