On Tue, Sep 13, 2016 at 11:10 AM, Niel Henriksen <shireham.gmail.com> wrote:
> Hi Dan,
>
> Can I set those through the pysander interface?
>
>
I think no. Those are some options:
https://github.com/hainm/amber_things/issues/21
you need to change pysander code for that:
https://github.com/Amber-MD/pysander/blob/master/sander/src/pysandermodule.c
Hai
> --Niel
>
> On Tue, Sep 13, 2016 at 7:53 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi Niel,
> >
> > Did you explicitly set PME parameters in your input (nfft1 etc)? If
> > you make sure those are explicitly set you should get better
> > agreement.
> >
> > -Dan
> >
> > On Tue, Sep 13, 2016 at 10:34 AM, Niel Henriksen <shireham.gmail.com>
> > wrote:
> > > Hi Hai and Jason,
> > >
> > > Thanks for the troubleshooting advice. I tried both suggestions.
> Rather
> > > than read in the trajectory, via imin=5, I just did a single step
> energy
> > > calculation on a netcdf restart file.
> > >
> > > Sander EEL: -8225.6990
> > > pt.energy_decomposition elec: -8225.7691
> > > sander.energy_forces elec: -8225.6986
> > >
> > > So going through pysander directly is indeed a closer match. Any
> concern
> > > about the remaining difference? I can send you the files directly if
> you
> > > would like.
> > >
> > > Thanks,
> > > --Niel
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> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Sep 13 2016 - 09:30:02 PDT
