[gmx-users] hello

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 18 11:56:21 CEST 2012

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:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list