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Determine steps to export to LAMMPS format #570
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Quick thoughts:
|
The shortest term is going through InterMol, since InterMol can already convert to LAMMPS. |
Mostly, yes. Virtual sites will be supported soon. Other things can be extended when we reach them. We just need to map what OpenFF is doing onto LAMMPS. |
Here is a primitive prototype that demonstrates the above idea. It's not elegant but demonstrates that the basic idea is possible without too much hacking. (Note that it's not yet clear if this is generally feasible, but one step in that direction). Notable pain points here are how to keep track of positions before leaving OpenFF/OpenMM world and the strange dropping of a residue name somewhere along the way. This pipeline should later on be re-imagined to take in a clearly-defined data structure/chemical topology; this just builds up a single molecule from scratch. Rename the file |
This effort has moved to the Interchange project, which provides an export to LAMMPS. It is not yet battle-tested and is under active development, but it does well enough on the bare minimum case presented a few comments above. In:
Out:
0.015 kJ/mol energy differences do not pass the default tolerances I've assigned in the comparison method, but I'd argue it's a workable error given the feature provided and that the valence terms are within tolerance here. I'll still be working to improve this and other test cases. Please direct future issues relating to LAMMPS interoperability with OpenFF force fields here: https://github.com/openforcefield/openff-interchange/issues |
Thanks, Matt! |
There's a variety of reasons the nonbonded energies could be different because of how the bonded interactions - we should discuss a bit. Should I create an issue on the interchange project on resolving this? |
Yes, that sounds great! I suspect it is related to openforcefield/openff-interchange#159 but I have yet to isolate it - please feel free to add to that issue or open a new one. |
Is your feature request related to a problem? Please describe.
In order to integrate SMIRNOFF-format FFs into OpenKim's benchmarking framework, we will need to specify a simulation engine to run OpenFF calculations. OpenKim is willing to use OpenMM if needed, but would prefer to use LAMMPS, since that's widely used across their stack.
Describe the solution you'd like
A working code example, starting from a molecule file (for example,
1_cyclohexane_1_ethanol.pdb
), and producing the input files needed to run a LAMMPS simulation. This will almost certainly use ParmEd or InterMol.If possible, we should identify what aspects of the System are preserved vs. lost, for example periodic box dimensions, electrostatic and Lennard Jones cutoffs, and nonstandard 1-4 scaling.
Describe alternatives you've considered
If this ends up being unreliable or it is difficult to preserve the relevant information, then OpenKim is OK with us using OpenMM.
Tagging @mattwthompson who has some previous experience with LAMMPS and parameter conversion, and @yafshar from OpenKim.
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