Hi,
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.
http://www.cell.com/biophysj/fulltext/S0006-3495%2811%2902284-3
Cheers
Tom
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.
Best,
Michael
On Sun, Aug 19, 2012 at 3:16 PM, David Ackerman <da...@cornell.edu> wrote:
Hello,
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,
David
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