[gmx-users] Hexamer problem

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 5 21:06:05 CEST 2011

errabah fatima ezzahra wrote:
>  I will really appreciate any help of suggestions.I am doing simulation 
> of six monomers of identical helical peptide. the experiment literature 
> say that the peptides in a aqueous  solution should form a hexamer. so i 
> have done simulations for the six peptides under normal conditions with 
> T of 300k and the result are two trimer that are perpendicular with each 
> other.
> I don't know that to do to get the monomers rearrange and form a 
> heaxamer instead of two trimers.

You haven't said how long your simulations are, but such processes are likely to 
take quite some time.  You may need extensive simulation or some fortuitous 
starting configuration to actually produce this behavior.  If the literature 
measures the kinetics of such a process, then you have a baseline for what you 
might expect; keep in mind that atomistic MD simulations are generally only 
feasible on the submicrosecond time frame.



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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