AMBER Archive (2006)

Subject: AMBER: water diffusion

From: Sergei Smirnov (snsm_at_praseo.nmsu.edu)
Date: Mon Jul 17 2006 - 19:48:59 CDT

Hi,

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
Tel:(505)646-1547
Fax: (505)646-2649
http://www.chemistry.nmsu.edu/~etrnsfer
http://www.chemistry.nmsu.edu/smirnov_new.html

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