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 <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *À :* errabah fatima ezzahra <errab...@yahoo.fr
<mailto:errab...@yahoo.fr>>; Discussion list for GROMACS users
<gmx-users@gromacs.org <mailto: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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--
========================================
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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