[gmx-users] Smaller Area Per Lipid for DPPC Bilayer

[David Ackerman]

Hello,

I have been basing some DPPC bilayer simulations off of files from
Justin Lemkul's tutorial, including the .itp files and .mdp files.
Everything has been working fine except that my area/lipid seems to be
too low and my diffusion coefficient seems to be too slow compared to
experimental values. As a test, I just started with Tieleman's
equilibrated 128 DPPC bilayer system, including the waters, and ran a
simulation using the mdp file below (note though I selected
continuation=yes, this was in fact not continued from a previous
equilibration). The simulation has been running for ~75 ns so far, and
the area/lipid is on average ~.61-.62 nm^2 . When I do full
temperature/pressure equilibrations, even using different
thermostats/barostats, I seem to get area/lipid values similar to
these. Also, my diffusion coefficients are smaller than those reported
in papers invovling DPPC bilayers. I was wondering what the possible
reasons for this could be. Any help you could provide would be great.


Thanks,
David




; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000000
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 5000          ; save coordinates every 2 ps
nstvout         = 5000          ; save velocities every 2 ps
nstxtcout       = 5000          ; xtc compressed trajectory output every 2 ps
nstenergy       = 5000          ; save energies every 2 ps
nstlog          = 5000          ; update log file every 2 ps
; Bond parameters
continuation    = yes           ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cels
nstlist         = 5             ; 10 fs
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.12          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = Nose-Hoover   ; Less accurate thermostat
tc-grps         = DPPC SOL      ; three coupling groups - more accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 323   323     ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = semiisotropic         ; uniform scaling of x-y box
vectors, independent z
tau_p           = 1.0           ; time constant, in ps
ref_p           = 0.0 1.0               ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5   4.5e-5       ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off
;dihre = yes
;dihre_fc = 100
;dihre_tau = 0.0
;nstdihreout =50
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm         = 1
comm-mode       = Linear
comm-grps       = DPPC SOL