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

[Mehdi Bagherpour]

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.
>
> Now I am wandering if you could advise me a method to solve this problem.
>
> I would appreciate your help.
> Looking forward to hearing from you.
>
> Cheers,
> Bagherpour
>