Thank you!
On Tue, Oct 29, 2013 at 5:24 PM, Brian Radak <radak004.umn.edu> wrote:
> Three methods come to mind:
>
> 1) use cpptraj to strip out all but the atoms you want
>
> 2) use parmed to make a new prmtop with the only the interactions you want
>
> 3) if the energy is only a function of a few distances, extract those and
> recompute it by hand
>
> All of those energies will likely be slightly different if you are using
> PME, since then the energy isn't strictly pairwise in the reciprocal sum.
>
> Regards,
> Brian
>
>
> On Tue, Oct 29, 2013 at 4:37 PM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > I was wondering whether it is possible to read and MD trajectory and
> > calculate the energy between two groups of atoms, for instance, between
> two
> > nearby amino acids. From the manual, it seems that imin=5 will read the
> > trajectory and output the energy of the whole system. Can one select the
> > atoms for which Amber should calculate the energy?
> >
> > -Jose
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
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Received on Wed Oct 30 2013 - 06:00:04 PDT
