Simulating DNA in vacuum

From: C. Ecker (ecker_at_physik.hu-berlin.de)
Date: Fri Nov 14 2003 - 08:47:54 CST

Hi Namd-List!

Is any one of you experienced with simulation of DNA in vacuum ? I tried
to simulate a 12bp strand but found that even at very low temperatures the
dna is not stable. I observe after 10ps that 8 of the initially 22 h-bonds
between the bases are broken and the whole double helix is deformed. One
base even stucks out of the cylinder. This is for T=1K !

I know that simulating DNA in vacuum has been a problem in the early years
of MD. Is this still the case with namd ?

Thanks,
Christof

Humboldt-Universitaet zu Berlin
Institut fuer Physik
Physik von Makromolekuelen
Newtonstra▀e 15
D-12489 Berlin

fon: +49-30-2093 8030
fax: +49-30-2093 7632

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