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

[tarak karmakar]

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,

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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
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Any suggestions would be appreciated.

Thanks,
Tarak