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
========================================
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