I'm not very familiar with pysander, so I'm not certain - maybe Hai
can comment further.
Alternatively if there is a way to see what values pysander sets you
can input those back into the imin=5 run.
-Dan
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?
>
> --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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> 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
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Received on Tue Sep 13 2016 - 08:30:03 PDT
