[gmx-users] Hexamer problem

[Justin A. Lemkul]

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
> 
> ========================================
> 
> 

-- 
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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

========================================