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

[Joel Jose Montalvo Acosta]

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