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On 5/6/19 6:47 AM, Sankaran SV . wrote:
@email on Membrane protein Simulation: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html Dear Najamuddin Memon Thanks for your reply. I am a little confused here. Why is the protein alone drifting? Typically, when we simulate protein only or protein-ligand systems, the protein along with the co-molecule drifts – and hence we do pbc correction. But in our case, we observed that the lipid does NOT move. Only the protein, which is supposedly embedded in the lipid, drifts.
This is not true. Everything moves. Visualize any individual lipid and you will see it diffuse over time. Lipid diffusion timescales are extremely long, though, so net movement is much lower. But the protein is certainly capable of drifting (again, along with everything else) and is simply the most prominent species that is the most obvious to have changed its position.
Further, when we proceeded with centering the system with respect to the protein (which removed the drift), and calculated the number of water molecules that remained in the interface layer (defined as 4.5 angstrom from the protein) throughout the simulation, the two numbers were different. That is, we obtained 16 waters molecules that remained in the interface layer BEFORE centering and only 5 were found to be in the interface layer AFTER centering. Would centering affect the number of water molecules that resides in the hydration layer throughout the simulation?
Centering doesn't affect anything, just visualization convention. You need to be sure you're performing a robust calculation, but you haven't shown us how you're doing it so it's not possible to give more precise advice.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
