[gmx-users] Re: Error in DNA-Simulation

[Justin Lemkul]

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

-- 
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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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