On 11/4/12 7:01 AM, Mehdi Bagherpour wrote:
On Sun, Nov 4, 2012 at 2:38 PM, Mehdi Bagherpour
<[email protected]>wrote:
Dear all,
I used Gromacs to Simulate DNA(15bp) with CHARMM27 force-field in 50ns
.My sistem has about 10000 water molecules and outside of the DNA and the
edge of the box is 1nm. At the end of simulation the DNA is destroyed.
I used 8 processor system for simulation.
My mdp files for NVT,NPT,MD and last snap-shot pdb file is attached.
The list does not allow attachments, so you will have to provide a link to where
these files can be downloaded, or otherwise better describe what "destroyed"
means. If the two DNA strands appear to have come apart, this is likely a
periodicity effect and is correctable using trjconv.
-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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