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