On 2011-07-29 07:25:08AM -0500, Justin A. Lemkul wrote: > > > Peter C. Lai wrote: > > I was looking at the g_membed paper recently, and noticed the authors "only" > > spent 10ns to re-equilibrate the membedded-system after g_membeding. > > This they also did after bumping the temperature from 300 to 323K "to > > prevent > > ordering of the bilayer" even though the "typical" simulation temperatures > > of > > POPC is 300 to 310K...Anyone know why 323K was used? Was it to compare it > > to the DOPC environment or something? > > > > I can't comment on this, but it seems odd to me, too. > > > I noticed for my particular system, I had to run a round of EM on the > > post-membedded system in order to resolve some clashes before I could > > mdrun. > > Then I ran 10ns in NPT with gen_vel=yes at 310K and position restraints on > > the helix CA atoms. I am inferring that because the membrane patch I used > > had > > been previously equilibrated after I constructed it and ran it under NPT at > > 300K for 100ns, 10ns should be sufficient time to re-equilibrate with the > > protein in the middle and 310K temperature? > > > > I generally find that membrane protein systems need at least 20 ns or so to > really be equilibrated, but perhaps your system is a bit different. 10 ns is > about the shortest time you can use to start seeing translational relaxation > (rotational relaxation of lipids is shorter, roughly 5 ns).
Well I picked 10ns since the authors of g_membed claim that their g_membed packs so well (at least compared to say, inflateGRO) *shrug*. In fact, they claim that you can re-equilbrate in only 1ns after g_membed. In addition to APL, they measured deuterium order parameter and the density profile of water in z-axis columns, but they didn't elaborate on these other 2 metrics... > > > After the 10ns with protein restrained, I ran Grid_MAT on it and got a > > reasonable APL (61-62A^2/lipid when taking protein atoms into account, > > comparable to pre-g_membed patch) and the box dimensions look stable. Is > > this sufficient to answer the abvove question? > > > > Could be. Seems reasonable. > > > Now I am going to be introducing a ligand to the protein. Is there a way to > > preserve any state, like velocities of all the previous atoms? I was > > thinking > > of the doing the EM while freezing everything but the ligand atoms and > > allowing the ligand to change conformation (like a docking refinement). > > After > > this, can I have the thermostat and barostat rescale the original velocities > > (and gradually heat the ligand) instead of reinitialising everything? > > > > I doubt it. By introducing new atoms into the system, you can't use a > checkpoint file any more so you lose the state you had before. You can > preserve > velocities in a .gro file, but I can't think of a reasonable way to have > those > read (while not having velocities for the ligand) and then heat up the > ligand. > You'd have to use "gen_vel = no" in conjunction with simulated annealing, > which > sounds like a recipe for instability. Is there any particular reason you > think > a specific set of velocities is required? Random sampling is all part of > running proper simulations, so you need multiple, independent states to > converge > to get a reliable result, anyway. > Yeah didn't think so, but worth a thought. Just trying to look ways to save computational time. Wolf et al (the g_membed authors) seem to suggest that if the structure is already close-to or at equilibrium, then it should take little to to re-equilibrate when you have minimal perturbation... -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
