PLUMED-NEST

Project ID: plumID:22.000
Source: plumed-common-2.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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=nm 
TIME
the units of time
=ps  
ENERGY
the units of energy
=kj/mol
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
=2.pdb
RANDOM_EXCHANGES
Set random pattern for exchanges. More details

ab48: 
COORDINATION
Calculate coordination numbers. More details
  
GROUPA
First list of atoms
=3045,3048,3049,3050,3826,3829,3830,3831  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5452,5453,5454,5455  
R_0
The r_0 parameter of the switching function
=0.45
The COORDINATION action with label ab48 calculates a scalar quantityab49: 
COORDINATION
Calculate coordination numbers. More details
  
GROUPA
First list of atoms
=3045,3048,3049,3050,3826,3829,3830,3831  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5471,5472,5473,5474  
R_0
The r_0 parameter of the switching function
=0.45
The COORDINATION action with label ab49 calculates a scalar quantityab50: 
COORDINATION
Calculate coordination numbers. More details
  
GROUPA
First list of atoms
=3045,3048,3049,3050,3826,3829,3830,3831  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5487,5488,5489,5490  
R_0
The r_0 parameter of the switching function
=0.45

The COORDINATION action with label ab50 calculates a scalar quantityanti1: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
R_0
The r_0 parameter of the switching function
=0.1  
STRANDS_CUTOFF
If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like
=1 
STYLE
 Antiparallel beta sheets can either form in a single chain or from a pair of chains
=inter
The ANTIBETARMSD action with label anti1 calculates the following quantities:
 Quantity   
 Description  
anti1.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti1.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdanti2: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=430,431,432,433,434,435,32,33,34,35,36,37 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
R_0
The r_0 parameter of the switching function
=0.1  
STRANDS_CUTOFF
If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like
=1 
STYLE
 Antiparallel beta sheets can either form in a single chain or from a pair of chains
=inter

The ANTIBETARMSD action with label anti2 calculates the following quantities:
 Quantity   
 Description  
anti2.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti2.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdcat_site: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=3043,3824
ab48_site: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5442,5456
ab49_site: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5456,5475
ab50_site: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5475,5491
dis_ab48: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cat_site,ab48_site
The DISTANCE action with label dis_ab48 calculates a scalar quantitydis_ab49: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cat_site,ab49_site
The DISTANCE action with label dis_ab49 calculates a scalar quantitydis_ab50: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cat_site,ab50_site
The DISTANCE action with label dis_ab50 calculates a scalar quantity