thanks for your help
fatima-ezzahra
________________________________
De : Justin A. Lemkul <jalem...@vt.edu>
À : Discussion list for GROMACS users <gmx-users@gromacs.org>
Envoyé le : Mardi 5 Juillet 2011 15h35
Objet : Re: Re : [gmx-users] Hexamer problem
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 <jalem...@vt.edu>
> *À :* errabah fatima ezzahra <errab...@yahoo.fr>; Discussion list for GROMACS
> users <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
========================================
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
