5 ns is not long enough to equilibrate the APL, and it's a time-averaged property in experiment, so looking at one frame is not as good as averaging over tens of ns of simulation. Try running for 100 ns and taking the average of the last 50 ns. Also, what APL do you get and what value do you consider correct? Also look at the time-series of the APL to see if it is drifting in the right direction. I presume that you're computing APL as box_x * box_y / N lipids per leaflet (the per leaflet part obviously being important).
I think Tieleman was using a 0.9 nm LJ cutoff the last time he was working with the Berger lipids. Your 1.4 nm LJ cutoff is sure to decrease the APL in comparison to that. Finally, not all parameters give APL values that agree with experiment, so check the literature on your parameters (and cutoff) to see if at least you are getting something similar to what other people get. Other than the LJ cutoff, which is not necessarily wrong but at least could lead to differences, your mdp file looked fine to me. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of ali.khourshae...@student.sharif.edu <ali.khourshae...@student.sharif.edu> Sent: 08 February 2017 18:51:11 To: gmx-us...@gromacs.org Subject: [gmx-users] Problem with obtaining rational Area per lipid Dear Gromacs users, As part of my M.Sc. thesis I should do MD simulation. For this purpose, at first I intended to regenerate a rational Area per lipid with good agreement with experiment as verification of my subsequent MD simulations. I downloaded the initial .pdb file from Dr. tieleman lab website, Did a minimization and an Equilibration step. But, my final configuration failed to give a good Area per lipid. I wonder if you could have a very quick look on my .mdp files which is attached here and give some short comments on it. Also, it will be an asset for me it you could be able to share your .mdp file in minimization and equilibration stage with me regarding one of your published journal paper on lipid bilayer Eagerly looking forward to hear back from you. Sincerely, Ali ---------------------------------------------------------------------------------------------------------------------------------------------- Min.mdp integrator = steep ; emtol = 1000.0 ; emstep = 0.01 ; nsteps = 500 ; nstlist = 1 ; coulombtype = PME ; ns_type = grid ; rcoulomb = 1.0 ; rvdw = 1.4 ; pbc = xyz ; ---------------------------------------------------------------------------------------------------------------------------------------------- NPT. mdp integrator = md ; leap-frog integrator nsteps = 2500000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs nstxout = 0 ; save coordinates every 0.2 ps nstvout = 0 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = no ; 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 ns-type = grid ; search neighboring grid cels nstlist = 10 ; rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme-order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT tcoupl = V-rescale ; modified Berendsen 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 Pcoupl = Berendsen pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau-p = 0.25 0.25 compressibility = 4.5e-5 4.5e-5 ref-p = 1.0 1.0 pbc = xyz ; 3-D PBC gen-vel = yes ; assign velocities from Maxwell distribution gen-temp = 323 ; temperature for Maxwell distribution gen-seed = -1 ; generate a random seed nstcomm = 1 comm-mode = Linear comm-grps = DPPC SOL -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
