[gmx-users] hello

[Justin A. Lemkul]

On 6/18/12 5:46 AM, Anik Sen wrote:
> Hi This is Anik.
>
> Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The
> DNA consisted of a total 10 base pairs. But within the simulation the DNA is
> moving inside the solvation box and sometimes it is going outside of the box,
> though due to NVT simulation criteria the part going out from one side comes
> back from the other side. But the problem is in a certain step it looks awkward
> that part of DNA lying here and part lying there. I have taken bigger boxes but
> with the same result.
> Can anyone suggest how to overcome this problem? The interaction of the DNA with
> the water molecules may not hamper but it may not dance so much in the solvation
> box.
>

This topic seems to come up every day.  Consult the following page and/or the 
many recent threads in the list archive:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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