Hello I am trying to equilibrate from scratch a 196 POPC bilayer using Tom's charmm36.ff. My box has a lot of TIPS3P (charmm) waters above and below the membrane with a box size around 8.5x8.5x12.7. My desired end state is to only use the setup for g_membed but I'd also like to get a pristine tall bilayer that might be useful for other things or colleagues. I ran 1ns NPT so far with:
dt = 0.002 continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = POPC SOL tau_t = 0.5 0.5 ref_t = 300 300 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 DispCorr = no comm_mode = Linear comm_grps = POPC SOL The metrics look roughly stable: Energy Average Err.Est. RMSD Tot-Drift --------------------------------------------------------------------- Temperature 300 0.00018 0.957697 0.000466096 (K) Density 1017.26 0.24 1.5953 1.4803 (kg/m^3) Pressure 1.00795 0.065 99.5783 -0.0431925 (bar) Box-X 8.58491 0.036 0.0773839 -0.235388 (nm) Box-Y 8.59611 0.036 0.0774849 -0.235696 (nm) Box-Z 12.4357 0.1 0.216337 0.659896 (nm) My APLs are ~10A^2/lipid above what they "should be" according to Klauda and experimental (I get 76-77A^2/lipid vs 65-58A^2/lipid). I suppose with TIPS3P water, I could get closer LJ packing if I turned on DispCorr but I thought that you generally left that off in charmm36 bilayer runs... Now, I also could extend for several ns until density/box drift gets smaller, but any other thoughts (yes this is probably a continuation of the CHARMM36 lipid bilayers thread from October (http://www.mail-archive.com/[email protected]/msg34582.html)? Thanks -- =============================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | =============================================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
