[gmx-users] When to use Dispersion Correction for Lipid Bilayers

[Thomas Piggot]

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 <da294 at 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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
Dr Thomas Piggot
University of Southampton, UK.