[gmx-users] Re: Error in DNA-Simulation
jalemkul at vt.edu
Sun Nov 4 13:57:52 CET 2012
On 11/4/12 7:01 AM, Mehdi Bagherpour wrote:
> On Sun, Nov 4, 2012 at 2:38 PM, Mehdi Bagherpour
> <mbagherpour7749 at gmail.com>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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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