Hi Albert, see my comments below
On Fri, Nov 10, 2023 at 6:31 AM Albert Gauss via AMBER <amber.ambermd.org>
wrote:
> Hi all,
>
> I've been using the amber99SB-ILDN FF in Gromacs for a while now. I
> hadn't really considered switching to a newer version until recently.
I think that would be good, this is a very old FF now and isn't necessarily
bad, but you should be using more recent/better models.
>
> It's worth noting that Gromacs doesn't officially ship with force field
> versions higher than 99SB, but I'm interested in exploring those
> options. Lately, I've been building my systems in Leap and then
> converting them via Parmed for the newer versions. However, I'm unsure
> about the reliability of these topologies. To gain a better
> understanding, I decided to calculate different energies for the same
> trajectory using all three force fields and compare the results. My
> primary concern is the shift in potential energies between these force
> fields.
yes they should be shifted, of course, and perhaps with some scatter as
well.
It might be good to do the same analysis in Amber to get "reference"
energies for the implementation.
> Additionally, I observed that the coulomb energies are
> consistent between 99SB and 14SB but differ from SB19.
>
This should not happen, there are no changes to the partial charges in
ff19SB.
I suspect an implementation problem, since that has been known to happen in
the past.
For example, see the correction published by Best et al due to faulty
ff99SB implementation in Gromacs
https://www.cell.com/biophysj/fulltext/S0006-3495(08)78586-2
I would recommend evaluating the energies in Amber to get "correct" ff19SB
energies.
> Overall, I would greatly appreciate any feedback on the differences I've
> mentioned and the overall reliability of the conversion procedure from
> Amber to Gromacs via Parmed.
>
> Thank you in advance for your insights and assistance.
>
>
> Best
>
> Albert
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Received on Fri Nov 10 2023 - 08:30:02 PST
