thanks for your help

fatima-ezzahra



________________________________
De : Justin A. Lemkul <jalem...@vt.edu>
À : Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu>
> *À :* errabah fatima ezzahra <errab...@yahoo.fr>; Discussion list for GROMACS 
> users <gmx-users@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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