[AMBER] Comparing FF Energies: 99SB/14SB/19SB translated with parmed to Gromacs

From: Albert Gauss via AMBER <amber.ambermd.org>
Date: Fri, 10 Nov 2023 12:30:29 +0100

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. 
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. Additionally, I observed that the coulomb energies are
consistent between 99SB and 14SB but differ from SB19.

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.


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Received on Fri Nov 10 2023 - 04:00:03 PST
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