[gmx-users] When to use Dispersion Correction for Lipid Bilayers
t.piggot at soton.ac.uk
Mon Aug 20 11:42:03 CEST 2012
In addition to the Michael's comments, I saw an interesting poster about
this sort of inclusion for the long-range van der Waals interactions at
the Biophysical Society annual meeting earlier this year. A link to the
abstract for the poster is below. I guess this should become available
in GROMACS at some point soon.
Michael Shirts wrote:
> Short answer -- use a dispersion correction if the force field was
> parameterized to include one. Make sure you use the cutoff that the
> lipid was parameterized for as well.
> Long answer -- neither on nor off is correct for a lipid bilayer. A
> dispersion corrections corrects for the fact that you are neglecting
> the r^-6 term at long range. However, it assumes an isotropic
> distribution outside the cutoff. Lipid bilayers have long range
> order, so a standard dispersion correction is inappropriate. The
> lipid properties will be cutoff dependent, which is not a very good
> thing. See PJ in't Veld, AE Ismail, GS Grest, J. Chem. Phys. 127,
> 144711 (2007) for a solution, using Ewald summation for the
> Lennard-Jones terms. This is in the works for Gromacs (and has been
> for a while), but might still be a while because it's a little lower
> on the to do list. Once methods like this are in, it will be possible
> to parameterize lipids that behave correctly.
> On Sun, Aug 19, 2012 at 3:16 PM, David Ackerman <da294 at cornell.edu> wrote:
>> I was wondering when it is appropriate to use Dispersion Correction
>> for lipid bilayers, or which setting (no, EnerPres, or Ener) is best.
>> I have seen it used in some discussions, and not used in others. As
>> for myself, I have simulated a DPPC bilayer. With DispCorr=EnerPres, I
>> get an area per lipid of ~.615 nm^2 (whereas other reported values are
>> closer to .64 nm^2) and slower diffusion than is reported. However,
>> when I don't have a DispCorr term, my area per lipid becomes ~.656
>> nm^2 and my diffusion more closely matches other reported values.
>> So, should DispCorr be used at all for bilayer simulations, and if so,
>> which type is most appropriate?
>> Thank you for your help,
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Dr Thomas Piggot
University of Southampton, UK.
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