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

Reply via email to