From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Aug 23 2017 - 19:16:51 CDT
Seems reasonable to me. The whole point to the restraints is to keep anything interesting from happening while you aren't explicitly looking at it (or analyzing it). Since the only thing unrestrained in the system is going to be water and ions, which move around pretty quickly due to their small size, you probably only need to equilibrate for under a nanosecond.
On 08/23/2017 06:03 PM, Arthur Vale wrote:
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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