I agree with Adrian, the Coulomb energy being off isn't related to recent
force fields.
One possible issue here might be using cpptraj to calculate the energies
for "Amber", that is most likely correct, but less well validated than the
actual MD codes. it might be worth checking to see if Dan Roe has seen this
thread, or maybe calculating "canonical" energies in sander to make sure
they match cpptraj.
On Fri, Jan 26, 2024 at 10:42 AM Adrian Roitberg via AMBER <
amber.ambermd.org> wrote:
> In principle, this is a question for the gromacs list, right ?
>
> The implementation in AMBER is the canonical one (although of course it
> might have bugs).
>
> If another program claims to have implemented the same force field, it
> is up to them to show they actually did.
>
> One more point, The SB force fields, as far as I know, have not touch
> the charges at all, so whatever the electrostatics implementation is in
> AMBER, it is not related to the force field itself, and this discrepancy
> must also show if you look at older force fields like ff94, etc.
>
> Maybe worth checking those.
>
> Adrian
>
>
> On 1/26/24 10:07 AM, Albert Gauss via AMBER wrote:
> > [External Email]
> >
> > 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Fri Jan 26 2024 - 08:00:03 PST
