The pictures are still missing. As a quick fix, you can find the results
here
https://ibb.co/wrCJ57c . Additionally, another picture related to
question II) can be found here: https://ibb.co/nLrcWw3
On 1/26/24 15:42, Albert Gauss via AMBER wrote:
> I'm very sorry for this mess. The markup caused issues in my initial
> email. I hope it works correctly this time.
>
>
> Hi all,
>
> 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.
>
> WHAT I DID
>
> In short:
> I compared the energy contributions of 99SB/14SB and 19SB force
> fields, calculated using Gromacs with topologies converted from Amber,
> with those calculated using cpptraj.
>
> Long story:
> For 99SB, 14SB, and 19SB, I built all topologies in Leap and employed
> amb2gro_top_gro.py to convert them into Gromacs topologies. A 500 ns
> simulation of a small protein (1770 atoms) was conducted in Gromacs,
> and the trajectory was utilized for all subsequent calculations. Water
> and ions were removed, and the trajectory was centered. In the Gromacs
> calculation, I applied no cutoff for nonbonded interactions (all
> cutoffs much larger than the system) and no neighbor list
> (verlet-buffer-tolerance = -1, nstlist=1, rlist=50). The same xtc
> trajectory was used for all calculations. All Amber calculations were
> executed using cpptraj and its energy command. Various energies were
> calculated for all three force fields in both Amber and Gromacs for
> comparison.
>
> RESULTS
> The results, presented in two columns, display the time series on the
> left and the distributions of energy differences on the right.
>
>
> QUESTION
> I)
> I am attempting to interpret the differences in Coulomb energies. The
> Coulomb short-range (SR) energies exhibit deviations of approximately
> 3 kJ/mol. Interestingly, when comparing the energies from this Gromacs
> run with another Gromacs run where I built the topology internally
> (FF99SB), the energies are identical. I verified the charges, and they
> are consistent. Would you deem this energy difference tolerable? Is
> there a possible explanation for this, such as variations in
> electrostatics implementations?
>
> II)
> Concerning the disparities in Coulomb 14 interactions, I observed that
> the difference diminishes when directly comparing energies from
> cpptraj with results from Gromacs using an internally built topology
> (FF99SB). Could there be something missing in the topology converted
> from Leap with amb2gro_top_gro.py? Is there any known information on
> this?
>
>
> Thank you in advance!
>
> Best
>
> Albert
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Received on Fri Jan 26 2024 - 07:30:01 PST
