AMBER: water diffusion

From: Sergei Smirnov <>
Date: Mon, 17 Jul 2006 18:48:59 -0600


I do not know whether it is an appropriate place to ask my question but I ran
out of options.

I've been trying to run MD of DNA in a periodic box using AMBER 99 implemented
in Hyperchem 7.52 and found that I could not mimic DNA denaturing. Then I ran
just water in a 20A x 20A x 20A box for 200 ps and found that at 300K it
behaved like a crystal (no diffusion, only libration). The water is apparently
implemented as TIP3P. Hypercube people told me that it is likely the intrinsic
property of this potential. Is it true?

I also tried anther force field, MM+, and saw a 'normal' water behavior their.

Any advice would be gretaly appreciated.
Sergei Smirnov
Department of Chemistry and Biochemistry
1175 North Horseshoe Dr.
New Mexico State University
MSC 3C, PO Box 30001
Las Cruces, NM 88003
Fax: (505)646-2649

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Received on Wed Jul 19 2006 - 06:07:09 PDT
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