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

Kirill Bessonov kbessonov at gmail.com
Sun Jul 19 05:34:20 CEST 2009

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

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?

You said also that tpbconv is obsolete, so how would I resume my run, in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) ?
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