[gmx-users] the DNA md simulation

[Banafsheh Mehrazma]

Dear Justin;
I specified the terminal residues in the *.mdp file, just like what in
my force field has (DNA.rtp) mentioned. I wonder if we should some
thing else with it? I mean, when I viewed my molecule with VMD, after
a 5 ns simulation, my terminal residues were not in front of each
other, they are slanted inward the helix.
I don't know, whether it is right or not!

Best regards
B.Mehrazma

On 2/1/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Banafsheh Mehrazma wrote:
>> Dear all;
>>
>> Through the MD simulation for a DNA, I wonder whether we should change
>> any options for the terminal bases or not.
>>
>
> What is it that you think you should change?
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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