[gmx-users] separation of two strands of DNA during of simulation

[David van der Spoel]

On 2010-05-29 13.30, shahab shariati wrote:
> Hi gromacs users
> I runing md simulation of DNA for 20 ns (5000 frame). I see trajectory
> during simulation. I see in some times, two strands of DNA are seprated.
> simulation now is in frame of 4600. is this state true and rational?
> any help will highly appreciated!
>
Probably periodic boundary conditions. Check manual.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se