[gmx-users] How to exclude atoms within the same molecule from an rdf.

João M. Damas jmdamas at itqb.unl.pt
Thu Nov 6 22:35:17 CET 2014

It's fairly "simple": generate a .tpr file with a nrexcl big enough to
exclude "self-counts" and give it to g_rdf through the -s flag.


On Thu, Nov 6, 2014 at 8:42 PM, Stella Nickerson <stella.nickerson at gmail.com
> wrote:

> I'm simulating a mixture of molecules (call them Molecules A, B, and C).
> The rdf between A and B and between A and C both look fine, but the one
> between A and A is crazy-looking. I assume this is because it's comparing
> atoms within the same molecule. I can't figure out how to exclude atoms in
> the same molecule from the rdf.
> Thanks,
> Stella
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

More information about the gromacs.org_gmx-users mailing list