Comments (4)
eric-jm-lang
commented on May 28, 2024
Regarding nrexcl, you are correct regarding the meaning.
From the manual:
nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away
A value of nrexcl=3 seems to be the default in Parmed for every type of molecule (see for example ParmEd/parmed/parameters.py) and it looks like it is indeed what is the default for small molecules and proteins.
Examples from the manual seem to suggest that for water it is possible to have nrexcl=1 which makes sense given the definition. It seems also logical to have nrexcl=0 in the case of monoatomic ions.
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chryswoods
commented on May 28, 2024
I've added a fix for this in the parser branch in Sire and issued a pull request to bring into devel (parser #211).
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chryswoods
commented on May 28, 2024
I've added a test to SireUnitTests that compares the energies of molecules loaded to and from Eric's files (the amber files and their equivalent from parmed). The test is SireIO/test_ambgro.py. It gives interesting results which show disagreement between the energies of the amber files, our gromacs files and also the parmed gromacs files. Interestingly, converting back from our gromacs to amber gives the same energy, and converting back from parmed gromacs to amber gives the same energy.
The results of this test are printed below. For each energy term there are five values:
- The energy from the original amber input files
- The energy from the gromacs files written by Sire (converted from the amber files)
- The energy from the gromacs files written by parmed (converted from the amber files by Eric)
- The energy from the amber files converted from the gromacs files written by Sire
- The energy from the amber files converted from the gromacs files written by parmed
Ideally, all 5 energies should be identical. This is not the case.
Strangely, the parmed energies don't agree with the amber energies...
The Sire energies agree better, but are also out for some (especially coulomb and bond)
The back-converted amber energies are equal, so 2 == 4 and 3 == 5. Strange.
E_{cljff}^{CLJ_{default}}: -74306.9958019629 -74307.18291528475 -74310.60385158383 -74307.18291528488 -74310.60385158383
E_{cljff}^{LJ_{default}}: 7349.263053051327 7349.039465757929 7352.289416002735 7349.039465757929 7352.2894160027345
E_{cljff}^{coulomb_{default}}: -81656.25885501422 -81656.22238104268 -81662.89326758657 -81656.22238104281 -81662.89326758657
E_{intraclj}^{CLJ_{default}}: -8846.926930404212 -1949818.138133785 -1949655.3796204112 -1949818.138133785 -1949655.3796204112
E_{intraclj}^{LJ_{default}}: -916.1663721393626 -916.1745560819411 -914.8952690047718 -916.1745560819411 -914.8952690047719
E_{intraclj}^{coulomb_{default}}: -7930.760558264848 -1948901.963577703 -1948740.4843514063 -1948901.963577703 -1948740.4843514063
E_{intraff}^{1-4[LJ]}: 972.1638654037595 972.162691737714 972.881505919929 972.1626909930478 972.8815064894559
E_{intraff}^{1-4[coulomb]}: 13803.918022937934 13803.918301064346 13804.323984910621 13803.918305721187 13804.323989568602
E_{intraff}^{1-4}: 14776.081888341694 14776.08099280206 14777.20549083055 14776.080996714234 14777.205496058057
E_{intraff}^{angle}: 231.70027096935198 231.70031094668428 240.10804588737886 231.70031031666485 240.10804706364388
E_{intraff}^{bend-bend}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{bond}: 106.8991145741713 67.6768473486908 87.93402512045354 67.6768473470172 87.93402512045421
E_{intraff}^{dihedral}: 2282.1984914864333 2282.1976724906235 2282.797793809015 2282.1976701332396 2282.797794328362
E_{intraff}^{improper}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{internal}: 17396.87976537165 17357.65582358806 17388.0453556474 17357.655824511156 17388.04536257052
E_{intraff}^{stretch-bend-torsion}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{stretch-bend}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{stretch-stretch}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{urey_bradley}: 0.0 0.0 0.0 0.0 0.0
E_{total}: -65757.04296699546 -2006767.6652254816 -2006577.9381163477 -2006767.6652245587 -2006577.9381094244
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chryswoods
commented on May 28, 2024
I have now fixed this. The issue is that my test was calculating the intramolecular energy of solvent (water) molecules, which was not zero for the gromacs files (both from Sire and parmed). Removing the intramolecular energy from the solvent molecules gives agreement between Amber and the Sire-produced gromacs files. There is still disagreement with the parmed-produced gromacs files. Given that the Amber files are the source of truth, I think that Sire is right and parmed is wrong...
E_{cljff}^{CLJ_{default}}: -74306.995801963 -74307.18291528491 -74310.60385158377 -74307.18291528473 -74310.6038515838
E_{cljff}^{LJ_{default}}: 7349.263053051328 7349.039465757929 7352.289416002734 7349.039465757929 7352.289416002736
E_{cljff}^{coulomb_{default}}: -81656.25885501433 -81656.22238104284 -81662.8932675865 -81656.22238104267 -81662.89326758654
E_{intraclj}^{CLJ_{default}}: -8846.926930404212 -8846.934007427151 -8846.41453633516 -8846.934007427151 -8846.41453633516
E_{intraclj}^{LJ_{default}}: -916.1663721393626 -916.1745560819411 -914.8952690047718 -916.1745560819411 -914.8952690047718
E_{intraclj}^{coulomb_{default}}: -7930.760558264848 -7930.7594513452095 -7931.519267330388 -7930.7594513452095 -7931.519267330388
E_{intraff}^{1-4[LJ]}: 972.1638654037595 972.1626917377141 972.881505919929 972.1626909930478 972.8815064894559
E_{intraff}^{1-4[coulomb]}: 13803.918022937934 13803.918301064346 13804.323984910623 13803.918305721187 13804.323989568602
E_{intraff}^{1-4}: 14776.081888341694 14776.08099280206 14777.205490830553 14776.080996714234 14777.205496058057
E_{intraff}^{angle}: 231.70027096935206 231.70031094668443 240.10804588737864 231.7003103166649 240.10804706364408
E_{intraff}^{bend-bend}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{bond}: 67.67795199698396 67.67684734869087 87.93402512045357 67.67684734701722 87.93402512045417
E_{intraff}^{dihedral}: 2282.1984914864324 2282.197672490623 2282.7977938090135 2282.1976701332414 2282.7977943283654
E_{intraff}^{improper}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{internal}: 17357.65860279446 17357.65582358806 17388.0453556474 17357.65582451116 17388.04536257052
E_{intraff}^{stretch-bend-torsion}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{stretch-bend}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{stretch-stretch}: 0.0 0.0 0.0 0.0 0.0
E_{intraff}^{urey_bradley}: 0.0 0.0 0.0 0.0 0.0
E_{total}: -65796.26412957275 -65796.461099124 -65768.97303227153 -65796.46109820073 -65768.97302534844
(I've updated the test so that now it passes - it does not include a fail if the parmed files disagree)
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