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
problem.
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You said also that tpbconv is obsolete, so how would I resume my run, in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:
http://oldwiki.gromacs.org/index.php/Extending_Simulations
-Justin
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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