On Thu, Feb 21, 2002, Prabal Maiti wrote:
> I am trying to do dynamics of a double crossover DNA molecules (there is
> crossover between two double helix at specific location). There are 76
> base pairs. I have solvatd the systems and added Na+ ions. I could do
> minimization hloding the DNA fixed (ntr=1). After 8000 minimzation steps
> when I try to do NVT dynamics (still holding the DNA fixed) and gradually
> try to increase the temp. to 300 (below is the ctl file), I get even after
> 11 ps too many warning for vlimit exceed. It seems the solute temparature
> is too high in th erange of 10000k whereas solvent in the range 300K.
Sounds like you may have some bad energetics in the DNA. You should check
the coordinates carefully, and see if the potential energy is falling
during the simulation (sounds like it is, by a lot). It is typical
to continue restraints on the solute durnig the equilibration, but this
won't really help if you have very bad energies.
I know this isn't very specific, but you will need to examine your system
carefully yourself. If you are new to amber, you might think about starting
with a smaller system -- what you describe is bigger than any DNA system
I have seen simulated. But when the temperature goes to 10,000 K, it's
seldom just a matter of one variable being typed in wrong.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Sat Feb 23 2002 - 22:03:24 PST
