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
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