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 < montalvo...@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 <sp...@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. 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