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
Received on Tue Sep 13 2016 - 08:00:04 PDT
