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

[tarak karmakar]

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