Frankie Montenegro wrote:
On 9/11/07, David van der Spoel <[EMAIL PROTECTED]> 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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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