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

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 28 13:24:14 CEST 2010



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

Always equilibrate under the conditions you wish to use prior to collecting data 
under those conditions.

As for whether or not your force field is even valid at such high temperature is 
another question, but I know there is a substantial body of literature regarding 
high-temperature MD, so you may want to do some reading to understand the pros 
and cons of what you're trying to do.

-Justin

> shahid
> 
>  
> On 4/27/10, *Justin A. Lemkul* <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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-- 
========================================

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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