PLUMED-NEST-TEST-SITE

Project ID: plumID:24.033
Source: Plumed-nest/7q4b/plumed_reconstruct.dat
Originally used with PLUMED version: 2.6
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

#RESTART
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=structure_renumbered.pdb

# define all heavy atoms using GROMACS index file
The MOLINFO action with label  calculates somethingproteinThe GROUP action with label protein calculates the following quantities:
 Quantity   
 Type   
 Description  
protein
atoms
indices of atoms specified in GROUP: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein

# make protein whole
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-627 ENTITY1the atoms that make up a molecule that you wish to align=628-1254 ENTITY2the atoms that make up a molecule that you wish to align=1255-1881 ENTITY3the atoms that make up a molecule that you wish to align=1882-2508 ENTITY4the atoms that make up a molecule that you wish to align=2509-3135 ENTITY5the atoms that make up a molecule that you wish to align=3136-3762 ENTITY6the atoms that make up a molecule that you wish to align=3763-4389 ENTITY7the atoms that make up a molecule that you wish to align=4390-5016 ENTITY8the atoms that make up a molecule that you wish to align=5017-5643 ENTITY9the atoms that make up a molecule that you wish to align=5644-6270 ENTITY10the atoms that make up a molecule that you wish to align=6271-6897 ENTITY11the atoms that make up a molecule that you wish to align=6898-7524 ENTITY12the atoms that make up a molecule that you wish to align=7525-8151 ENTITY13the atoms that make up a molecule that you wish to align=8152-8778 ENTITY14the atoms that make up a molecule that you wish to align=8779-9405 ENTITY15the atoms that make up a molecule that you wish to align=9406-10032 ENTITY16the atoms that make up a molecule that you wish to align=10033-10659 ENTITY17the atoms that make up a molecule that you wish to align=10660-11286 ENTITY18the atoms that make up a molecule that you wish to align=11287-11913 ENTITY19the atoms that make up a molecule that you wish to align=11914-12540 ENTITY20the atoms that make up a molecule that you wish to align=12541-13167 ENTITY21the atoms that make up a molecule that you wish to align=13168-13794 ENTITY22the atoms that make up a molecule that you wish to align=13795-14421 ENTITY23the atoms that make up a molecule that you wish to align=14422-15048 ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file

DUMPATOMSDump selected atoms on a file. More details STRIDE the frequency with which the atoms should be output=1 FILEfile on which to output coordinates; extension is automatically detected=traj_7q4b.gro ATOMSthe atom indices whose positions you would like to print out=protein
DUMPMASSCHARGEDump masses and charges on a selected file. More details FILEfile on which to output charges and masses=mcfile ATOMSthe atom indices whose charges and masses you would like to print out=protein