Hello, I am trying to simulate a DPPC bilayer, 180 lipids total, ~13000 TIP3 and 50 K, 50 Cl counter-ions. The standard charmm27r DPPC parameters have very large charge groups, so I went through them and made them smaller (4 atoms each, on average), following the comments from grompp. I have tried the C27 parameters, recent parameters by Sonne, et al. (Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension. Jacob Sonne, et al. Biophysical Journal, 15 June 2007. Vol. 92, Issue 12, pp. 4157-4167) as well as the latest Charmm36 parameters available from Alex MacKerrell's website. The last two do not require surface tension so I was using semiisotropic pressure coupling with the same compressibility for XY and Z (4.5e-5). For charmm27 parameters I set XY compressibility to 0 (constant area).
I am using all-bond constraints with LINCS and the CHARMM_TIP3P water model. I have tried langevin dynamics as well as the standard md integrator. The temperature is coupled separately for DPPC and non-DPPC at 323.15K. When I run any simulation for >10 ns, I get what looks like frozen lipids. They become very straight and aligned with each other, sometimes intercalated. I'm not sure why this is happening... It may be that the lipids are using incorrect dihedral and/or angle parameters (only charges are set explicitly in my DPPC ITP files, everything else is in the base ffnb.itp) Any guesses as to why this may be happening? Anything specific I should be analyzing? I see a steady decrease in LR coulombic potential which seems to change depending on my fourierspacing... so I wonder if my PME settings are wrong. Here is part my MDP: integrator = sd define = -DCHARMM_TIP3P nsteps = 500000000 dt = 0.002 bd-fric = 0 ld-seed = -1 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 1000 xtc-precision = 1000 nstcomm = 5 nstcalcenergy = 5 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rcoulomb = 1.3 pme_order = 6 ewald_rtol = 1e-5 vdwtype = Switch rvdw = 1.3 rvdw_switch = 1.0 rlist = 1.3 rlistlong = 1.5 fourierspacing = 0.12 tc-grps = DPPC non-DPPC tau_t = 1 1 ref_t = 323.15 323.15 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = yes gen_temp = 323 gen_seed = -1 constraints = all-bonds constraint-algorithm = Lincs lincs-iter = 1 lincs-order = 6 lincs-warnangle = 60 morse = no -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
