[gmx-users] creating trajectory with ligand close to the protein

David Osguthorpe David.Osguthorpe at uchsc.edu
Sun Feb 24 02:00:49 CET 2008


Can anybody tell me what is the best way to re-write a trajectory run with periodic boundary
conditions such that a molecule (eg. the protein) is chosen as the reference
and every other molecule in the system (eg. ligands) is transformed such that its periodic
image closest to the reference molecule is chosen.

Ive been using trjconv but it seems to be failing for a case where the protein switches
image in the trajectory but the ligand does not.



More information about the gromacs.org_gmx-users mailing list