PLUMED-NEST

Project ID: plumID:20.027
Source: MetaD_analysis.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

#PLUMED script to output the C-CA-CB-CG and CA-CB-CG-CD2 dihedral angles of His41 in SARS-CoV1/CoV2 Mpro
#Also outputs the His41-Nepsilon to Cys145-Sgamma atomic distance as dyad_dist and the His41-NHdelta to Glu166 carboxyl salt bridge interaction distance 

t1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=607,609,612,618
The TORSION action with label t1 calculates a scalar quantityt2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=607,609,612,620
The TORSION action with label t2 calculates a scalar quantitydyad_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=616,2241
The DISTANCE action with label dyad_dist calculates a scalar quantitysaltbrdg_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2554,2640

The DISTANCE action with label saltbrdg_dist calculates a scalar quantity
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,t2,dyad_dist,saltbrdg_dist 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=COLVAR_Tor