[gmx-users] Re: Hexamer problem

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
> Hi All;
> 
>  I did run simulation for 6 proteins for 200ns and the protein is just 
> 18 residue each (have 6 of them)  so 108 residues. i did run the 
> simulation in constant pressure then with Temperature 650K (for 20 ns) 
> to make sure that are separate and then run the simulation of the 
> proteins with 300K Temperature for 200ns. I am supposed to get a hexamer 
> but still giving me two trimers that are perpendicular to each other.
> does any body have an idea why this is happening?/
> 

Are you sure you have trimers, or do you have a hexamer that is split across a 
periodic boundary, making it appear as if you have two trimers?

Also realize that (1) a single trajectory cannot be consider conclusive and (2) 
200 ns is still "short" by in vitro/in vivo standards.  Again, I have no clue 
what time frame you should expect, but it is an important caveat.

-Justin

> Thank you so much for your help
> 
> Fatima-ezzahra
> 
> 
> 
>  >
>  > ------------------------------------------------------------------------
>  > *De :* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *À :* errabah fatima ezzahra <errabahf at yahoo.fr 
> <mailto:errabahf at yahoo.fr>>; Discussion list for GROMACS users 
> <gmx-users at gromacs.org <mailto: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
> 
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

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

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

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