PLUMED-NEST

Project ID: plumID:20.027
Source: MetaD_script.dat
Originally used with PLUMED version: 2.5
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

#RESTART
#PLUMED script to perform metadynamics for torsions of the CA-CB-CG-CD2 dihedral angle of His41 in SARS-CoV-1/CoV-2 MPro

t1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=607,609,612,618

#Metadynamics setup - Gaussian of height 0.1 kJ/mol with adaptive bias width - geometric scheme
The TORSION action with label t1 calculates a scalar quantitymetad: 
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
=t1 
SIGMA
the widths of the Gaussian hills
=0.05 
HEIGHT
the heights of the Gaussian hills
=0.01 
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=GEOM 
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.000000001 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.1 
PACE
the frequency for hill addition
=500 
FILE
 a file in which the list of added hills is stored
=HILLS_His41Tor

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=t1,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR_His14Tor