[gmx-users] Re: Hexamer problem/ high and low salt solutions.

Thu Jul 7 15:27:22 CEST 2011

Hi everybody

 i did Againrun the simulation for 2000ns and the proteins were just moving every were , they were forming the two rimers but not for along time like in the simulation with the 200ns and 20 ns.

Justin : i did check the periodic boundary using VMD and it does not to seem to be the case. thank you 

so I am thinking about running the simulation in diferrent solutions like low salt , high salt and organic solvent ... I am new to gromacs and i only used water to solvate the system and wondering if using different pH solution and different salt concentration solution  is something possible to do . i did some research and found out that you can add ions like NA+ and CL_ but i was wondering if anybody does have an idea of some solution that already have a pH known or solutions with high salt concentaration that i can use instead of water when solvaiting the system.

please any suggestion will be appreciated 

thank you

fatima-ezzahra

________________________________
De : Justin A. Lemkul <jalemkul at vt.edu>
À : Discussion list for GROMACS users <gmx-users at gromacs.org>
Envoyé le : Mercredi 6 Juillet 2011 10h01
Objet : [gmx-users] Re: Hexamer problem

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

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