[gmx-users] Pushing MD further

[Berk Hess]

Hi,

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.

Berk

> 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
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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