[gmx-users] lower Area per lipid for DPPC with CHARMM36

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================