Dear GROMACS users, I am trying to calculate the potential of mean force (PMF) of a molecule (A) across phospholipid bilayer (LIP) using constraint method. I am using GROMACS ver 4.0.4. RUN parameters are as follows ------------------------------------------------------------------------------- integrator = md tinit = 0 dt = 0.002 ;[ps] nstlist = 10 ;[step] ns_type = grid rlist = 1.0 pbc = xyz
coulombtype = pme rcoulomb = 1.0 ;[nm] epsilon-r = 1 ;(1) vdw-type = switch rvdw-switch = 0.9 ;[nm] rvdw = 1.0 ;[nm] DispCorr = EnerPres fourierspacing = 0.12 ;[nm] (0.12) fourier_nx = 0 ;(0) fourier_ny = 0 ;(0) fourier_nz = 0 ;(0) pme_order = 4 ;(4) ewald_rtol = 1e-05 ;(1e-5) epsilon_surface = 0 ;(0) optimize_fft = no tcoupl = berendsen tc_grps = LIP SOL A tau_t = 0.1 0.1 0.1 ;[ps] ref_t = 300 300 300 ;[K] Pcoupl = berendsen Pcoupltype = semiisotropic ;useful for membrane tau_p = 1.0 1.0 ;[ps] compressibility = 4.5e-05 4.5e-05 ;[bar^-1] ref_p = 1.0 1.0 ;[bar] gen_vel = no ;yes or no gen_temp = 300 ;[K] gen_seed = 113 ;(173529) constraints = all-bonds ;all-bonds/none constraint-algorithm = LINCS unconstrained-start = no lincs-order = 4 ;(4) lincs-warnangle = 30 ;(30) ; COM PULLING pull = constraint pull_geometry = direction pull_dim = N N Y pullstart = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = LIP pull_group1 = A pull_vec1 = 0.0 0.0 -1.0 pull_init1 = -3.50 pull_rate1 = 0 pull_k1 = 500 ------------------------------------------------------------------------------- When I simulated under above parameters, following warnings and errors were generated. -Warning: pressure scaling more than 1% -LINCS warning: These errors were always generated when a molecule (pull_gropu1) was existing in water phase. After simulation, serious disruption of a molecule (pull_gropu1) was observed. However, when a molecule (pull_gropu1) was existing inside lipid membrane, no error was observed and calculation was successfully conducted in constrained simulation. I have done long time (5 nsec) simulations before constrained simulation using umbrella method, thus I believe the initial condition is fully equilibrated. Could some one please give me an advice to calculate PMF? Sincerely ___________________________________________________________________ Hideya Nakamura, Ph.D. Post Doctoral Associate University of Florida, Particle Engineering Research Center (PERC) mail to: [email protected] _______________________________________________ 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
