[gmx-users] Re: Enthalpy Confusion

[David van der Spoel]

On 2013-06-14 21:39, Jeffery Perkins wrote:
>> Your calculation seems correct. Which gmx version did you use?
>> The correlation between the numbers is almost 100% so there must be a
>> simple explanation.
>
> gmx version is 4.5.4, and yeah the correlation is odd, in the code you
> listed:

Then that is the reason. I forgot about it, but the calculation of pv is 
incorrect in that version. If you use 4.5.7 or 4.6.2 it should be fine.
>
>>>               pv = vol*md->ref_p/PRESFAC;
>>>
>>>               add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
>>>               enthalpy = pv + enerd->term[F_ETOT]
>
> so pv = vol * md->ref_p/PRESFAC; is the vol * ref_p/conversion factor,
> right?
> the only thing there that seems like it could be off is if PRESFAC isn't
> correct for some reason
>
> (correct me if I'm wrong of course!)
>
> Jeffery
>
>
>
> --
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>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se