On 2/15/15 7:39 AM, tarak karmakar wrote:
Dear All, All atom simulation of DPPC bilayer (128 lipids) is resulting a low area per lipid (sliding down from ~58 to ~54 in 4 ns NPT). I'm performing the simulation in gromacs-5.0.4 with the charmm36 force field parameters for the lipid molecules. The NPT.mdp is pasted bellow,
We've been discussing this exact topic in another thread for days... Your .mdp settings are wrong. http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM -Justin
------------------------------------------------------------------------------------------------- title = NPT production for cxcr_WT ; Parameters describing the details of the NVT simulation protocol integrator = md ; Algorithm ("md" = molecular dynamics [leap-frog integrator]; "md-vv" = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 5000000 ; Number of steps to run (0.002 * 500000 = 1 ns) ; Parameters controlling output writing nstxout = 10000 ; Write coordinates to output .trr file every 2 ps nstvout = 10000 ; Write velocities to output .trr file every 2 ps nstenergy = 10000 ; Write energies to output .edr file every 2 ps nstlog = 10000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) vdwtype = switch rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rvdw_switch = 0.8 pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) ; Parameters for treating bonded interactions continuation = no ; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 1 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = Nose-Hoover ; Modified Berendsen thermostat using velocity rescaling tc-grps = DPPC SOL_Ion ; Define groups to be coupled separately to temperature bath tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps) ref_t = 300 300 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT conditions pcoupltype = semiisotropic ; Isotropic scaling in the x-y direction, independent of the z direction tau_p = 5.0 ; Coupling time constant (ps) ref_p = 1.0 1.0 ; Reference pressure for coupling, x-y, z directions (bar) compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility (bar^-1) ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel = no ; Velocity is read from the previous run ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 ; COM removal frequency (steps) comm_mode = Linear ; Remove COM translation (linear / angular / no) comm_grps = DPPC SOL_Ion ; COM removal relative to the specified groups ----------------------------------------------------------------------------------------------------------- Any suggestions would be appreciated. Thanks, Tarak
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.