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
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 __________________ You said also that tpbconv is obsolete, so how would I resume my run, in other words what is the best way to resume?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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