Comments (4)
mrshirts
commented on August 27, 2024
1
That's literally all one does, change the masses in the [ atoms ] section.
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mattwthompson
commented on August 27, 2024
@mrshirts as far as I can tell, based on your comment in the other thread and a couple of forum posts, this is as simple as modifying the masses in the [ atoms ] section of each molecule. Anything I should look out for, or anything official here?
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mattwthompson
commented on August 27, 2024
Awesome, thanks for the guidance. I have a quick patch started that should take care of this, i.e. here's an ethanol with hydrogen masses set to
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.500000 0.833333
[ atomtypes ]
;type, bondingtype, atomic_number, mass, charge, ptype, sigma, epsilon
MOL0_0 6 12.01078 0.0000000000000000 A 0.337953176162662 0.4553891161106184
MOL0_1 6 12.01078 0.0000000000000000 A 0.337953176162662 0.4553891161106184
MOL0_2 8 15.99943 0.0000000000000000 A 0.2997159987248637 0.8764372596155737
MOL0_3 1 1.007947 0.0000000000000000 A 0.2644543413268124 0.06602135607582665
MOL0_4 1 1.007947 0.0000000000000000 A 0.2644543413268124 0.06602135607582665
MOL0_5 1 1.007947 0.0000000000000000 A 0.2644543413268124 0.06602135607582665
MOL0_6 1 1.007947 0.0000000000000000 A 0.2583225710839196 0.068656285380106
MOL0_7 1 1.007947 0.0000000000000000 A 0.2583225710839196 0.068656285380106
MOL0_8 1 1.007947 0.0000000000000000 A 0.0534539230883669 5.157198260534728e-05
[ moleculetype ]
MOL0 3
[ atoms ]
;index, atom type, resnum, resname, name, cgnr, charge, mass
1 MOL0_0 1 MOL0 C 1 -0.097099998345 5.609843039231
2 MOL0_1 1 MOL0 C 1 0.131429998825 7.743488692820
3 MOL0_2 1 MOL0 O 1 -0.601339997103 13.865784346410
4 MOL0_3 1 MOL0 H 1 0.044759998719 3.141592653590
5 MOL0_4 1 MOL0 H 1 0.044759998719 3.141592653590
6 MOL0_5 1 MOL0 H 1 0.044759998719 3.141592653590
7 MOL0_6 1 MOL0 H 1 0.017319998393 3.141592653590
8 MOL0_7 1 MOL0 H 1 0.017319998393 3.141592653590
9 MOL0_8 1 MOL0 H 1 0.398090003679 3.141592653590
...
Still needs tests, etc. but I think this passes the eye check
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mattwthompson
commented on August 27, 2024
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Related Issues (20)
- PACKMOL wrapper with >100,000 atoms HOT 6
- Make `Interchange.topology` required? HOT 1
- LAMMPS atom writer makes assigning unique IDs to chemically-identical molecules impossible HOT 3
- Support writing to file-like objects
- `ligand_in_water/ligand_in_water.ipynb` example is failing on openff-docs HOT 2
- JSON roundtrip doesn't work with `from_openmm` generated system HOT 2
- `from_openmm` doesn't take `System` masses HOT 3
- Bond information is silently lost in openmm roundtrip for constrained systems HOT 5
- Document known limitations of `Interchange.from_openmm`
- ENH and/or DOC: Better handling of atoms with resindex 0 in GROMACSAtom HOT 6
- Improve GROMACS export speed HOT 18
- Unique atom types in LAMMPS. HOT 6
- Improve handling of residue IDs/numbers in GROMACS files HOT 7
- Add basic performance tests
- GROMACS export crashes due to non-bonded lookup failures when virtual sites are present in some topologies HOT 2
- GROMACS Residue IDs not incremented when writing multiple copies of a unique molecule
- Status of vacuum simulations in GROMACS HOT 5
- Loosing Gromacs atom name details when using an OpenMM topology HOT 5
- Protein water systems HOT 1
- Add `Interchange.to_amber`
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