On Wed, Dec 18, 2002, Andrei Leitão wrote:
> I am doing a molecular modeling study (500ps) to a DNA
> decamer including explicit solvent molecules (H2O) and
> counterions (Na+) at constant pressure.
>
> I made a molecular dynamic at 300K without this heating
> procedure and one of the end base pairs was very distorted
> from the axis.
Take a look at the equilibration procedure in the DNA tutorial on the
Amber web site. Two comments on your system:
(a) don't use constant pressure until the system is already heated up
at constant volume;
(b) generally, one should heat and equilibrate with constraints to the
initial structure (set ntr=1); after that is done, you can remove the
constraints.
In spite of all of this, it is not unusual (or necessarily wrong) to see
an end base-pair distorted from the axis (although I don't know what you
really mean by "very distorted"...)
..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 Wed Dec 18 2002 - 11:42:51 PST
