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? 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. Thank you for your help Joel Montalvo Acosta PhD student at University of Strasbourg -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.