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

[David Osguthorpe]

Hi,

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.

Thanks

David