[gmx-users] DMPC diffusion: G54A7

[David van der Spoel]

On 2012-02-10 16:14, Jon Kapla wrote:
> Dear users,
>
> I'm trying out the relatively new phospholipid parameters from Poger et.
> al. 2010 (DOI: 10.1002/jcc.21396), by simulating a box of a DMPC bilayer
> and approx. 30 SPC water molecules per lipid. I'm getting very low
> lateral diffusion compared to both other force fields (like Berger) and
> experimental data.
>
> The topology, force field (G54A7) and a preequilibrated box of DMPC and
> water are all downloaded from ATB (http://compbio.biosci.uq.edu.au/atb/)
> and corrected according to mail conversations with Poger himself (only
> some names that needs to be swapped in the itp file to make it fit the
> pdb).
>
> The latest simulations I performed at 315K gave me a lateral diffusion
> coefficients between 1.2*10^-8 cm^2/s and 2.5*10^-8 cm^2/s depending on
> treatment of electrostatics and simulation length (from 50 to 350 ns).
> These numbers are around ten times smaller than numbers typically
> reported for similar systems at similar temperatures (and also raising
> the temperature to 350K increases the diffusion by a factor of 2 or 3).
>
> Does anyone have any clue of what (if anything) I might be doing wrong?
>
> I paste the contents of a typical input file below, I have tried to be
> as close to what Poger used in his paper as possible (using PME instead
> of RF though). I've tried some different cutoffs for rlist (0.8, 0.9 and
> 1.4) and rcoulomb (0.9,1.4) but nothing of that seems to influence the
> diffusion much.

In fact RF sometimes make diffusion faster than PME but sometimes slower 
too. It always has an impact. See e.g. J. Chem. Theory Comput., 2006, 2 
(1), pp 1–11.

>
> Thank you!
>
> Kind regards,
> Jon Kapla
>
> RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
> nsteps = 50000000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; Part index is updated automatically on checkpointing (keeps files
> separate)
> simulation_part = 1
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 10
> ; group(s) for center of mass motion removal
> comm-grps = upper lower SOL
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 2500
> nstvout = 2500
> nstfout = 0
> ; Output frequency for energies to log file and energy file
> nstlog = 500
> nstcalcenergy = -1
> nstenergy = 500
> ; Output frequency and precision for .xtc file
> nstxtcout = 0
> xtc-precision = 1000
> ; This selects the subset of atoms for the .xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 5
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc = xyz
> periodic_molecules = no
> ; nblist cut-off
> rlist = 0.8
> ; long-range cut-off for switched potentials
> rlistlong = -1
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 1.4
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch = 0
> rvdw = 1.4
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = no
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Seperate tables between energy group pairs
> energygrp_table =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
> ;
> Tcoupl = berendsen
> tc-grps = DMPC SOL
> tau_t = 0.1 0.1
> ref_t = 315 315
> ld_seed = -1
> ;
> Pcoupl = berendsen
> Pcoupltype = Semiisotropic
> tau_p = 1.0 1.0
> compressibility = 4.6e-5 4.6e-5
> ref_p = 1.0 1.0
> ;
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen_temp = 315
> gen_seed = 173529
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> ; Type of constraint algorithm
> constraint_algorithm = Lincs
> ; Do not constrain the start configuration
> continuation = no
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 4
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 1
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 30
> ; Convert harmonic bonds to morse potentials
> morse = no
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se