Hi Justin, Still there is some problem. In the short equilibration I've got the good value of the Area per lipid. But now in the production run, it kept on decreasing. Presently, the value is ~56 A^2. The following .mdp has been used.
---------------------------------------------------------------------------------------------------------------------------------- title = NPT 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 = 1000 ; Write output to .log file every 2 ps ; 7.3.9 Neighbor Searching nstlist = 10 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb = 1.2 ; [nm] distance for Coulomb cut-off fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb DispCorr = no ; 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 = 323 323 ; 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) ; Initial Velocity Generation gen_vel = no ; Velocity is read from the previous run 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 ; Parameters for treating bonded interactions constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) 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) continuation = no ; Whether a fresh start or a continuation from a previous run (yes/no) ---------------------------------------------------------------------------------------------------------------------------------- Any suggestion would be helpful. Thanks, Tarak On Mon, Feb 16, 2015 at 4:01 PM, tarak karmakar <tarak20...@gmail.com> wrote: > Oh! Thanks. :) > Sorry I should have checked it before running the simulation. > Now, I'm getting APL ~62.5 A^2 which is pretty good compared to the expt. > > > > On Sun, Feb 15, 2015 at 6:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> 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. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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