[gmx-users] Pushing MD further
gmx3 at hotmail.com
Fri Nov 20 16:11:38 CET 2009
I would think any system with a membrane in it is too large to gain much with REMD
(unless you are interested in the temperature dependence).
You can use essential dynamics sampling or flooding, see make_edi.
> Date: Fri, 20 Nov 2009 10:00:11 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Pushing MD further
> Thielges, Sabine wrote:
> > Hi,
> > I am currently running some GPRC MD with membrane. After a lot of trial
> > I now have a nice 25 ns run with an agonist. But the final structure is
> > too close the starting and I know it is far from what the biology
> > describes.
> > I would like to know if there is options that I can add to my md.mdp
> > file to make the MD "explores some other area".
> There is no magic .mdp option to make sampling better, and you can not
> necessarily ever trust the results of just one single simulation. There are
> several options to enhance sampling:
> 1. Simulated annealing
> 2. Replica-exchange MD
> 3. Additional simulations with different starting velocities
> With #2, bilayers can be quite problematic. A recent paper from Max Berkowitz's
> group in JPCB has a nice protocol for REMD with a membrane.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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