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
--
========================================
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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