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