On Fri, Jan 26, 2024, Albert Gauss via AMBER wrote:
>>I have conducted comparisons for different energy contribution in
>>the 99SB/14SB and 19SB FFs using Amber and Gromacs. Between both
>>engines, I found most of the energies identical. However, I observed
>>deviations in the Coulomb SR and Coulomb 14 energies, and I’ve been
>>wondering at the reason.
How big is the system you are comparing? (1770 atoms seems way too big --
why not see what happens in a dipeptide?) Given what you have found, you
should create the smallest system you can that shows a difference.
You have a figure with bond energy differences. Start with that: you should
be able (in a small system) to look at each individual bond term, and try to
determine where the differences are.
For electrostatics, the same approach should be used. But I'd also
recommend first checking the fundamental constants in the two programs.
Conversion from kcal/mol to kJ/mol (4.184 exactly) should not be causing
problems, but the value used for the magnitude of the electron charge could
cause small discrepancies that could add up, since they are all in one
direction.
...good luck....dac
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Received on Fri Jan 26 2024 - 08:30:02 PST
