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 <[email protected]>
À : Discussion list for GROMACS users <[email protected]>
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 <[email protected] <mailto:[email protected]>>
> > *À :* errabah fatima ezzahra <[email protected]
><mailto:[email protected]>>; Discussion list for GROMACS users
><[email protected] <mailto:[email protected]>>
> > *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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