Actually I don't recall exposing those variables through the C API. So
you'd need to fix *that* before even thinking about addressing the Python
API.
However, for exactly the same input (same box size, etc.), you should get
exactly the same default PME parameter assignments. Can you run the sander
API tests and see if those pass? Those test cases reproduce regular sander
results exactly, if I recall correctly (well, out to the 4 decimal places
reported in the mdout file).
I'm not particularly concerned about the 0.0004 kcal/mol disagreement here
in one term, though. Especially for single-point energies. But it
*should* be identical out to 4 decimal places, so it would be interesting
to see why it's not...
All the best,
Jason
On Tue, Sep 13, 2016 at 12:06 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > 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
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 13 2016 - 09:30:02 PDT
