[gmx-users] Peptide - DMPC membrane simulations -> Unstable system

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 19 13:42:05 CEST 2009

Kirill Bessonov wrote:
> Hi Justin,
> I am running now peptide in DMPC as I figured out the main source of the 
> problem. This is my main goal: to see how this peptide interacts with 
> DMPC. I had done couple of videos on preliminary trajectory. Check them 
> out here http://www.youtube.com/watch?v=KX6XOGfCzQ0 and 
> http://www.youtube.com/watch?v=QwntHk8hBH8

It would be nice, for archival purposes, to post what the solution was to your 

> So you suggest to run position restrained dynamics by including:
> define = -DPOSRES
> in the .mdp run file. But in this case I would not allow peptide to 
> diffuse into DMPC as it will be freezed... Actually, I do not know what 
> molecule (protein or the DMPC, water) will be freezed. Could you tell me 
> why did you suggested position restrained dynamics and why it is good, 
> as I think it is less "realistic" simulation. Where can I get more info 
> position restrained dynamics to understand it better?

I didn't suggest that you use position restraints during data collection.  It is 
common practice to run an equilibration phase first, typically with position 
restraints on the protein, to allow the surrounding solvent to equilibrate.  In 
this case, you have a heteregeneous solvent, with water and lipids present, both 
of which are interacting with your protein.  This period of time is discarded; 
unrestrained simulations are used for data collection.  For membrane systems, 
this period of time can be several (if not 10-20) ns in length, because you are 
taking a pre-equilibrated structure and changing it pretty substantially by 
introducing a protein.

> __________________
> You said also that tpbconv is obsolete, so how would I resume my run, in 
> other words what is the best way to resume? Use tpbconv but with input 
> index file (-n flag) ?

See here:



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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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