Reference in documentation

[a-ws-m]

Hi @orbeckst , I had a question about this section of the docs: https://mdpow.readthedocs.io/en/latest/fep.html#differences-to-published-protocols
Can you send the reference to the Mobley paper you mention, please?
Also, intuitively I suspect that for the sake of the partition coefficient, there should be no need to do the vacuum calculation because it would cancel out when one takes the difference in free energies. But I'm getting very spurious results so perhaps that's wrong, hence why I'd like to review the paper.

[orbeckst]

This looks like a very old piece of the docs as it mentions GROMACS 4.x... I am afraid I don't remember which paper I referred to (should have written it down at the time!) — probably one of the earliest SAMPL papers from @dmobley's group.

There are issues with couple-intramol = no related to cut-offs, see

MDPOW/mdpow/templates/bar_charmm.mdp

Lines 47 to 50 in 120c5dd

	; WARNING: GROMACS <2021 incorrectly deals with exclusions. See https://gitlab.com/gromacs/gromacs/-/issues/3403
	; GROMACS >= 2021 requires rlist >= diameter of solute for couple-intramol = no FEP calculations
	; In order to set rlist to a fixed value, disable the automatic verlet buffer with -1.
	; by UNCOMMENTING THE NEXT LINE and INCREASE rlist AS NECESSARY.

(but I haven't looked at what the latest state there is).