From: Arthur Vale (arthurovale_at_uchicago.edu)
Date: Wed Aug 23 2017 - 18:58:59 CDT
We have a pre-equilibrated membrane, which we used for putting a protein on top, solvating and ionizing. Since we already equilibrated the membrane by itself, we were thinking of just restraining the heavy atoms of the membrane with 2.5 or 1 as the K for the constraining, and 10 for the protein backbone, starting at the target temperature and pressure, and then (after minimization) scaling the restrains down in steps until we reach 0 as scaling factor. We just wanted to check if this sounds like a reasonable protocol for running a pre-equilibrated membrane with a protein. We would also be happy to receive suggestions on what are typical protocols for running pre-equilibrated membranes.
Thank you in advance for the help,
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