PLUMED-NEST

Project ID: plumID:20.015
Source: 3-ANALYSIS/3.1-ASSEMBLE-XTC/plumed_driver.dat
Originally used with PLUMED version: 2.6-dev
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

# include topology info
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
=../../0-TOPO/step5_charmm2gmx.pdb 
WHOLE
 The reference structure is whole, i

# define all atoms
The MOLINFO action with label  calculates somethingprotThe GROUP action with label prot calculates the following quantities:
 Quantity   
 Type   
 Description  
prot
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=../../0-TOPO/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=PROT

# make protein whole
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 ...
ADDREFERENCE
 Define the reference position of the first atom of each entity using a PDB file
EMST
 Define atoms sequence in entities using an Euclidean minimum spanning tree
ENTITY0
the atoms that make up a molecule that you wish to align
=1-6701
ENTITY1
the atoms that make up a molecule that you wish to align
=6702-6741
... WHOLEMOLECULES

# PRINT ATOM POSITIONS
DUMPATOMS
Dump selected atoms on a file. More details
 
STRIDE
 the frequency with which the atoms should be output
=1 
FILE
file on which to output coordinates; extension is automatically detected
=traj.gro 
ATOMS
the atom indices whose positions you would like to print out
=prot