Hi I haven't played with gromacs in years, so I'm pretty new at the ability to play with large systems like lipid bilayers.
What is the "correct" or lets say canonical method to equilibrate a membrane patch of say 9x9 nm POPC with sufficient vertical waters to take care of pbc and long range interactions (> 1.5nm above/below the bilayer) using Tom's Charmm36 FF port. I am seeing a lot of different methods out there to: construct and equilibrate such a system in prepration for g_embed or whatever. I see from http://www.mail-archive.com/gmx-users@gromacs.org/msg33812.html the ability to use genbox to replicate Tieleman's 128 patch but I also can build my bilayer inside VMD, which supports charmm36->pdb atom names (and things seem to work fine) I have yet to see anybody's run parameters and constraints for running the equilibration, particularly using charmm36 (using vdwtype=switch). Should I constrain all heavy atoms in the lipid during the NVT run, or just the polar group (or even just P) and allow the tails to "melt" as seen elsewhere? Should I only set Z axis constraints? How long should I run in NVT before switching to NPT and for how long (10ns?) And should I change the constraints moving from NVT to NPT? How should the thermostat be coupled? System or separate the water from the lipid? I experienced the same thing as Ng Hui Wen back in October with waters being extremely dehomogenized (and diffusing out of the box) after 100ps NVT with all heavy POPC constrained at 1000 kJ/nm for all axes. I am sure that moving to NPT will restore the waters but still it was a bit scary to see for the first run. If a lot of these approaches haven't been published, maybe we can just stick them in the wiki to let everyone "pick their poison" when it comes to equilibrating their bilayers. Thanks for any ideas/hints/suggestions -- =============================================================== 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
