[gmx-users] Pushing MD further

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 20 16:00:11 CET 2009

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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