[gmx-users] lower Area per lipid for DPPC with CHARMM36
tarak karmakar
tarak20489 at gmail.com
Sun Feb 15 13:39:37 CET 2015
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,
-------------------------------------------------------------------------------------------------
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
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