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

[Dries Van Rompaey]

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