Hi Dan,
Can I set those through the pysander interface?
--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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Received on Tue Sep 13 2016 - 08:30:03 PDT
