[gmx-users] Hexamer problem

[errabah fatima ezzahra]

 thanks for your help

fatima-ezzahra



________________________________
De : Justin A. Lemkul <jalemkul at vt.edu>
À : Discussion list for GROMACS users <gmx-users at gromacs.org>
Envoyé le : Mardi 5 Juillet 2011 15h35
Objet : Re: Re : [gmx-users] Hexamer problem



errabah fatima ezzahra wrote:
> Hi justin
> 
> Thank you so much for your help,  my simulation did run for 40 mins, 1000000 steps,  20000.0 ps. . is that enough or should i do longer simulations

I already suggested you look into the literature for what you might expect for a reasonable time frame.  Intuition would say that 20 ns is far too short, but that's a complete guess and up to you to evaluate.

-Justin

> Thank you
> 
> fatima Ezzahra
> 
> ------------------------------------------------------------------------
> *De :* Justin A. Lemkul <jalemkul at vt.edu>
> *À :* errabah fatima ezzahra <errabahf at yahoo.fr>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Envoyé le :* Mardi 5 Juillet 2011 15h06
> *Objet :* Re: [gmx-users] Hexamer problem
> 
> 
> 
> 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
> 
> -- ========================================
> 
> 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
> 
> ========================================
> 
> 

-- ========================================

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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