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
# include topology info 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=../../0-TOPO/step5_charmm2gmx.pdb WHOLE The reference structure is whole, i
# define all atoms prot : 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)=../../0-TOPO/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=PROT # make protein whole WHOLEMOLECULESThis 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 only for backward compatibility, as of PLUMED 2 ENTITY0the atoms that make up a molecule that you wish to align=1-6701 ENTITY1the atoms that make up a molecule that you wish to align=6702-6741 ... WHOLEMOLECULES
# PRINT ATOM POSITIONS 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.gro ATOMSthe atom indices whose positions you would like to print out=prot