VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Mon Jul 08 2024 - 01:38:32 CDT

Dear Joel,
W dniu 7.07.2024 o 12:35, Joel Subach pisze:
> Hello VMD Community:),
>
> towards the above-topic, should I discard any of my QM optimized water
> interaction positions that settle into an area greater than a few
> angstroms from the interaction site?
If the water is repelled, then there is no interaction energy minimum at
the interaction site. Often, the interaction site was incorrectly
classified in FFTK as a donor while it should be an acceptor, or vice
versa. An example when this happens is with the nitro group, because
FFTK always considers nitrogen an acceptor and in -NO2 it is actually
positively charged.

Otherwise, if the water is several angstroms away, the interaction
energy would be very small and inclusion of such result in the charge
optimization would just drive the respective partial charge close to
zero. In my opinion, it may only be useful when the interaction site is
indeed nonpolar and you need enough water interactions to prevent the
charge fitting to be under determined. An example when this is the case
is when the interaction site is a nonpolar hydrogen.
Cheers,
Pawel

>
> Thanks if you know:),
> Joel 🚀 

-- 
Room 3.03 A-3, tel. +48 71 320 3200
email: Pawel.Kedzierski_at_pwr.edu.pl
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Wrocław University of Science and Technology
Wrocław, Poland