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

[Mark Abraham]

David Osguthorpe wrote:
> 
> 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.

Check out trjconv -h, and if none of the options works, please describe 
why they're failing :-)

Mark