[gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

[David van der Spoel]

Frankie Montenegro wrote:
> On 9/11/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Frankie Montenegro wrote:
> 
>> That sounds difficult because computing volume is difficult. We should
>> write a better program for this, but the problem lies in definition:
>> where does one water molecule stop and the next begin?
>>
> 
> Thanks. I was hoping to use Voronoi volume for compressibility
> calculation. That should ensure that individual partial volumes add up
> to the complete volume. So, is any of the two (trjorder vs g_hbond)
> better?
but neither of these programs calculate volumes. for selecting the 
nearest waters trjorder is easiest.
> 
>> This is because of Berendsen coupling. It should be better with
>> Nose-Hoover or without (using shifted vdw potential as well).
> 
> I suspected Berendsen coupling might be the problem. Should I expect
> anything close to the measured value with Nose-Hoover, but keeping vdw
> the way it is?

I suggest you try both on pure water. Will take you half an hour.
> 
> Regards,
> Frankie
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se