[gmx-developers] trjconv defaults

David Osguthorpe david.osguthorpe at gmail.com
Fri Oct 17 17:34:07 CEST 2008

> I can't even count how many times there are e-mails on the users list
> where people complain that their ligand doesn't stay bound to the
> protein; usually it's pbc problems. (Perhaps it's a good idea to
> actually put a suggestion relating to this in the documentation?)

Id also like to second this - the right magic trick to get ligands
to be in their binding site is somtimes quite complicated
- cluster has worked for me but also gets into an infinite loop sometimes
- Im still running 3.3.1 to maintain numerical consistency - ie.
I can reproduce trajectories at the binary level


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