Free energy, annihilation: charged ligand

User discussions
1

GROMACS version: Any version
GROMACS modification: No

Dear Everyone,

it may be a naif question, but I am going to ask: what is exactly going on in the code when switching off charges and vdWs of a charged chromophore? I am wondering how PME is accounted for, as actually a, say, +1 charge is fading without any buffer ion appearing in its place. I am not getting any warning (at any of the lambda windows: neither the extremes nor the intermediate ones), but simply I wonder how. Starting from a neutralized box with the necessary counterions, all to me is just the same as the initial state (be it lambda = 0), but in the final lambda = 1 state, where the only thing that faded is the +1 charge. Thank you for your time!

Bests,
Jacopo

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There should be a warning if either of the end states are net charged. If that is not the case, could you open an issue at Issues · GROMACS / GROMACS · GitLab? Preferably with input files to reproduce it?

3

Thank you so much once again. Took me a while to answer as I wanted to furtherly verify once again, as well as prepare simple examples with reproducibility (made a script). Moreover, this very question came from my supervisor, he is opening the gitlab thread and we are going to provide three very simple examples soon