Hello, I have been basing some DPPC bilayer simulations off of files from Justin Lemkul's tutorial, including the .itp files and .mdp files. Everything has been working fine except that my area/lipid seems to be too low and my diffusion coefficient seems to be too slow compared to experimental values. As a test, I just started with Tieleman's equilibrated 128 DPPC bilayer system, including the waters, and ran a simulation using the mdp file below (note though I selected continuation=yes, this was in fact not continued from a previous equilibration). The simulation has been running for ~75 ns so far, and the area/lipid is on average ~.61-.62 nm^2 . When I do full temperature/pressure equilibrations, even using different thermostats/barostats, I seem to get area/lipid values similar to these. Also, my diffusion coefficients are smaller than those reported in papers invovling DPPC bilayers. I was wondering what the possible reasons for this could be. Any help you could provide would be great.
Thanks, David ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000000 dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 2 ps nstvout = 5000 ; save velocities every 2 ps nstxtcout = 5000 ; xtc compressed trajectory output every 2 ps nstenergy = 5000 ; save energies every 2 ps nstlog = 5000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; Less accurate thermostat tc-grps = DPPC SOL ; three coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 1.0 ; time constant, in ps ref_p = 0.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ;dihre = yes ;dihre_fc = 100 ;dihre_tau = 0.0 ;nstdihreout =50 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = DPPC SOL -- 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