Project ID: plumID:19.020
Source: step-1/plumed.6.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
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
=250
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
=383.528
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
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_WTE
ENDPLUMED
Terminate plumed input. More details