Gromacs Node #306
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Gromacs Node #306
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M-R-Schaefer
requested changes
Jul 12, 2024
for more information, see https://pre-commit.ci
M-R-Schaefer
requested changes
Jul 12, 2024
* added fudge factors * added converting trajectory to ase atoms * uncomment energy extraction * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update installation instructions * update installation instructions * Allow for external ITP / PDB files (#311) * allow external `itp_files` * support optional pdb files * create charges from smiles instead of PDB files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Fabian Zills <[email protected]> Co-authored-by: PythonFZ <[email protected]> Co-authored-by: Fabian Zills <[email protected]>
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M-R-Schaefer
approved these changes
Jul 26, 2024
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This PR implements a Node for classical sampling of configurations using https://github.com/alanwilter/acpype and the GAFF as well as PACKMOL and RDKit for generating boxes from smiles.
I've added some trajectory conversion utilities. The energy reading code works in principle but I am fairly certain that the energies I obtain are wrong in some way. There is also an issue that the gmx energy command works on the CLI but not from within the node so I have opted to set the energies to 0 for now.
TODO
maxwarn, currently identifiers don't seem to be unique