Hi Carlos,
thank you for your quick response, which I found very useful. I plan to
follow your advice and will share the results.
I'd like to ask one follow-up question.
Could you please briefly outline the reasoning for the observed energy
shifts and scattering?
Thanks a lot for your help.
Best,
Albert
On 11/10/23 17:04, Carlos Simmerling wrote:
> 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 Sun Nov 12 2023 - 13:30:02 PST
