[gmx-users] Trajectory correction for pbc before H-bond analysis

Erik Marklund erik.marklund at chem.ox.ac.uk
Tue Mar 15 10:20:39 CET 2016

Dear Agnivo,

No. g_hbond / gmx bond takes pbc into account, so you normally don’t need to bother with preprocessing your trajectory.

Kind regards,

> On 15 Mar 2016, at 01:09, Agnivo Gosai <agnivogromacs14 at gmail.com> wrote:
> Dear Users,
> I always do pbc correction for the trajectory before doing RMSD, Radius of
> Gyration and COM separation analysis for my protein-ligand complex.
> Is pbc correction recommended before doing H-bond analysis ? I have 20 long
> simulations and I need to do a quick H-bond analysis for them. So, I was
> thinking if I could skip that step for now.
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
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