[gmx-users] Long Range dispersion correction with Lennard-Jones PME

[Mark Abraham]

Hi,

All the details are in the reference manual, e.g. section 4.9.2

Mark

On Thu, Jul 21, 2016 at 6:21 PM Joel Jose Montalvo Acosta <
montalvo161 at gmail.com> wrote:

> Dear David,
>
> Thanks for your answer.
>
> Following the papers you suggested me (also a recent paper titled
> "Direct-Space Corrections Enable Fast and Accurate Lorentz− Berthelot
> Combination Rule Lennard-Jones Lattice Summation". JCTC 2015 *11* (12),
> 5737-5746.) plus your explanations I could understand a bit more the
> implementation of LJ-PME in Gromacs, at least in the case where geometric
> combination rule is used for both LJPME and the force field (as e.g.,
> OPLS).  However, I still have some questions about the use of arithmetic
> combination rule with LJPME.
>
> In a first case, when both the LJPME and the force field use the arithmetic
> combination rule (as Charmm FF), the dispersion correction is zero, because
> LJPME is exact in this condition and there is not need to apply any
> dispersion correction (this is the same result when geometric combination
> rule is used for both LJPME and force field as you indicated before),
> however this is impractical because the arithmetic combination rule for
> LJPME is very slow. Then, to have a good efficiency, LJPME should be used
> with the geometric combination rule even with force fields which use the
> arithmetic combination rule (as Charmm). In this second case, a very small
> dispersion correction is computed (as you indicated), but I still don't
> know how this contribution is obtained (I could not reproduce this value by
> hand using a model system), could you provide me more detail about the
> computation of <C6> and the dispersion correction for this case?. Also, Is
> it necessary to add this (small) dispersion correction for this second
> case?
>
> Thank you in advances,
>
> Joel
>
>
>
> 2016-07-20 19:21 GMT+02:00 David van der Spoel <spoel at xray.bmc.uu.se>:
>
> > On 20/07/16 17:01, Joel Jose Montalvo Acosta wrote:
> >
> >> Dear Gromacs users and developers,
> >>
> >> I want to understand how the long-range dispersion correction is
> >> implemented in gromacs when van der waals (vdw) interactions are
> computed
> >> with cut-off or PME, so I started reading the section 4.9.1 in the
> gromacs
> >> (version 5.1.2) manual to check the involved formulas. Then, I did some
> >> tests using a model system composed by 2 argon atoms and computing the
> >> Lennard-Jones (LJ) contribution applying cut-off (without shift the vdw
> >> potential, ie., using vdwtype=cut-off and vdw-modifier=none in the mdp
> >> file) with and without dispersion correction (DispCorr=Ener and
> >> DispCorr=no). After, I computed by hand the dispersion contribution to
> the
> >> potential energy for this system. Finally, the values for the dispersion
> >> contribution obtained from gromacs and by hand were equal.
> >>
> >> Next, I tried a second test with the same model and same conditions but
> >> using PME instead cut-off to treat the vdw interactions with and without
> >> the dispersion correction. In this second test, the dispersion
> >> contribution
> >>  computed by gromacs was 0. I expected this result because this
> correction
> >> is suitable when vdw interactions are computed with cut-off and the
> radial
> >> distribution function outside the cutoff is assumed equal to 1. Thus, I
> >> though it looks incompatible to use dispersion correction
> (DispCorr=Ener)
> >> and PME for computing vdw interactions.
> >>
> >> However, using a real system as a protein or ligand in water and
> applying
> >> PME and the dispersion correction for vdw interactions, gromacs is
> >> computing a dispersion correction contribution, which is unexpected
> >> according to the previous tests done before. For this system, gromacs
> >> prints in the log file the average dispersion constant (<C6>) which I
> >> could
> >> not reproduce manually following equation 4.169 in the gromacs (v.
> 5.1.2)
> >> manual. I don't know how gromacs is computing this <C6> value for this
> >> system with PME.
> >>
> >> Finally, My questions are:
> >> 1. How does gromacs compute the dispersion correction when vdw
> >> interactions
> >> are computed with PME?
> >>
> > The result for the dispersion correction with LJPME are zero when you use
> > a geometric combination rule, since the LJPME is exact in principle.
> > If you use the arithmetic combination rule (e.g. Charmm FF) and LJPME is
> > told to use the geometric combiation rule (for efficiency) the dispersion
> > correction estimates the difference in dispersion between the two.
> Usually
> > this number is very small.
> >
> > I suggest you read these two papers:
> > - Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical
> > Effects on Surface Tension and Lipid Properties
> > Christian L. Wennberg, Teemu Murtola, Berk Hess, and Erik Lindahl  J.
> > Chem. Theory Comput. 2013, 9, 3527−3537
> >
> > - Nina M. Fischer, Paul J. van Maaren, Jonas C. Ditz, Ahmet Yildirim and
> > David van der Spoel: Properties of Organic Liquids when Simulated with
> > Long-Range Lennard-Jones interactions J. Chem. Theory Comput. 11 pp.
> > 2938-2944 (2015)
> >
> > 2. Is it right to apply this correction when vdw interactions is computed
> >> with PME? if the answer is not, it would be nice if gromacs prints a
> >> warning message indicating this incompatibility when both options are
> >> used.
> >>
> >> More info would be good indeed.
> > Maybe you can file a documentation request on http://redmine.gromacs.org
> >
> >
> >> Thank you for your help
> >>
> >> Joel Montalvo Acosta
> >> PhD student at University of Strasbourg
> >>
> >>
> >
> > --
> > 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
> > --
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