[gmx-developers] trjconv defaults

Berk Hess hessb at mpip-mainz.mpg.de
Fri Oct 17 17:37:58 CEST 2008

We could implement a proper solution for this.

An option one would be:
-pbc nojump
center on protein
-pbc mol
But then all in one call of trjconv


David Osguthorpe wrote:
>> 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
> David
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