PLUMED-NEST

Project ID: plumID:21.037
Source: BANAL-52-103-CoV/BANAL-52-103-CoV.2/3-ANALYSIS/PLUMED/plumed_driver.dat
Originally used with PLUMED version: 2.7
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

# various backbone RMSD
# ACE
rmsd-ace:  
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=rmsd-ACE.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
NOPBC
 ignore the periodic boundary conditions when calculating distances
# RBD
rmsd-rbd: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=rmsd-RBD.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
NOPBC
 ignore the periodic boundary conditions when calculating distances
# INTERFACIAL rmsd
rmsd-inter: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=rmsd-INTER.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# salt bridges
# RCOO- group of ASP (D) /GLU (E)
# RHN3+ from LYS (K) or (RNHC(NH2)2+) of ARG
# D30-K417K - inter
s1-1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
the pair of atom that we are calculating the distance between
=188,10812
The DISTANCE action with label s1-1 calculates a scalar quantitys1-2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
the pair of atom that we are calculating the distance between
=187,10812
# K31-E35  - intra
The DISTANCE action with label s1-2 calculates a scalar quantitys4-1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
the pair of atom that we are calculating the distance between
=207,276
The DISTANCE action with label s4-1 calculates a scalar quantitys4-2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
the pair of atom that we are calculating the distance between
=207,275
# D38-K353 - intra
The DISTANCE action with label s4-2 calculates a scalar quantitys5-1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
the pair of atom that we are calculating the distance between
=313,5301
The DISTANCE action with label s5-1 calculates a scalar quantitys5-2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
the pair of atom that we are calculating the distance between
=312,5301

# print stuff
The DISTANCE action with label s5-2 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
=rmsd-ace,rmsd-rbd,rmsd-inter 
FILE
the name of the file on which to output these quantities
=COLVAR_RMSD 
STRIDE
 the frequency with which the quantities of interest should be output
=1
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=s1-1,s1-2,s4-1,s4-2,s5-1,s5-2 
FILE
the name of the file on which to output these quantities
=COLVAR_SB 
STRIDE
 the frequency with which the quantities of interest should be output
=1