[gmx-users] more than one peptide in one simulation box

[shahid nayeem]

Hi Justin
Should I try to do position restraint at 500k and then full MD simulation.
shahid


On 4/27/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> shahid nayeem wrote:
>
>> My peptide is 26 residue alpha helix obtained from crystal structure  .pdb
>> file. I am posting energy minimization, position restarint and full MD
>> simulation .mdp file
>>
>>
>
> <snip>
>
>
>> ref_t = 300 300
>>
>
> Here, you're equilibrating at 300 K...
>
> <snip>
>
> ref_t = 500 500
>>
>
> and here, you're running MD at 500 K, without any equilibration in between.
> That could be a problem, but more likely, the high temperature is simply
> causing the structure to break down.  Short helices are usually not stable
> in isolation, and heating them to extreme conditions will probably
> accelerate this process. The various results you're seeing with different
> helices may just reflect that you haven't simulated long enough to see
> convergence in the structural features, but from what you've described, I
> expect what you're seeing is entirely normal, and almost predictable.
>
> -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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