[gmx-users] Verlet scheme and relative free binding energy

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 2 16:16:17 CET 2016


One can vary PME parameters for electrostatics at approximately constant
accuracy by scaling the Fourier grid spacing and short-range cutoff by the
same factor. (This is what mdrun does during PME tuning.) So you can use
rcoulomb = 1.0 and spacing scaled accordingly.

In GROMACS 2016, the Verlet scheme will likely support specifying such
setups directly.


On Tue, Feb 2, 2016 at 3:19 PM Dries Van Rompaey <dries.vanrompaey at gmail.com>

> Hi gmx-users,
> I have a question regarding the correct treatment of cut-offs for
> amber99sb-ildn in relative free binding energy calculations, using the
> verlet scheme. Many articles seem to use a 1.2 nm cutoff for coulomb
> interactions and a vdw interaction switched off between 0.9 and 1 nm (for
> instance: DOI: 10.1039/c5sc02678d). However, this setup is only possible
> with the now deprecated group scheme.
> I haven't been able to find any papers using amber99sb-ildn for relative
> free energy calculations with a setup suitable for verlet scheme. Does
> anyone have experience with such a setup for relative free binding energy
> calculations?
> Thanks in advance,
> Dries
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