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

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 27 15:32:50 CEST 2010

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


> ref_t = 300 300

Here, you're equilibrating at 300 K...


> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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