PLUMED-NEST

Project ID: plumID:21.037
Source: BANAL-52-103-CoV/BANAL-52-103-CoV.3/3-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-aceThe RMSD action with label rmsd-ace calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd-ace
scalar
the RMSD between the instantaneous structure and the reference structure that was input:  
RMSD
Calculate the RMSD with respect to a reference structure. This action has hidden defaults. 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
rmsd-ace:  
RMSD
Calculate the RMSD with respect to a reference structure. This action uses the defaults shown here. 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
  
NUMBER
 if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here
=0
# RBD
rmsd-rbdThe RMSD action with label rmsd-rbd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd-rbd
scalar
the RMSD between the instantaneous structure and the reference structure that was input: 
RMSD
Calculate the RMSD with respect to a reference structure. This action has hidden defaults. 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
rmsd-rbd: 
RMSD
Calculate the RMSD with respect to a reference structure. This action uses the defaults shown here. 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
  
NUMBER
 if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here
=0
# INTERFACIAL rmsd
rmsd-interThe RMSD action with label rmsd-inter calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd-inter
scalar
the RMSD between the instantaneous structure and the reference structure that was input: 
RMSD
Calculate the RMSD with respect to a reference structure. This action has hidden defaults. 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
rmsd-inter: 
RMSD
Calculate the RMSD with respect to a reference structure. This action uses the defaults shown here. 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
  
NUMBER
 if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here
=0

# salt bridges
# RCOO- group of ASP (D) /GLU (E)
# RHN3+ from LYS (K) or (RNHC(NH2)2+) of ARG
# D30-K417K - inter
s1-1The DISTANCE action with label s1-1 calculates the following quantities:
 Quantity   
 Type   
 Description  
s1-1
scalar
the DISTANCE between this pair of atoms: 
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
s1-2The DISTANCE action with label s1-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
s1-2
scalar
the DISTANCE between this pair of atoms: 
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
s4-1The DISTANCE action with label s4-1 calculates the following quantities:
 Quantity   
 Type   
 Description  
s4-1
scalar
the DISTANCE between this pair of atoms: 
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
s4-2The DISTANCE action with label s4-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
s4-2
scalar
the DISTANCE between this pair of atoms: 
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
s5-1The DISTANCE action with label s5-1 calculates the following quantities:
 Quantity   
 Type   
 Description  
s5-1
scalar
the DISTANCE between this pair of atoms: 
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
s5-2The DISTANCE action with label s5-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
s5-2
scalar
the DISTANCE between this pair of atoms: 
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
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
The PRINT action with label  calculates something
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