Gromacs Node (#306)

* smiles2gmx draft

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* small changes - still wrong box size

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* address comments

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Added Trajectory conversion to GMX (#308)

* added fudge factors

* added converting trajectory to ase atoms

* uncomment energy extraction

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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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]>

* set tolerance for packmol

* set pbc to true

* bump tolerance

* do what ruff says

* add MDAnalysis as dev deps for testing

* improve gmx to ase

* bump znh5md

* clean up aux files

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Moritz R Schäfer <[email protected]>

ipsuite/configuration_generation/__init__.pyi

@@ -1,6 +1,13 @@
 """Module for generating new configurations based on smiles."""
 
+from .gmx import Smiles2Gromacs
 from .packmol import MultiPackmol, Packmol
 from .smiles_to_atoms import SmilesToAtoms, SmilesToConformers
 
-__all__ = ["SmilesToAtoms", "Packmol", "SmilesToConformers", "MultiPackmol"]
+__all__ = [
+ "SmilesToAtoms",
+ "Packmol",
+ "SmilesToConformers",
+ "MultiPackmol",
+ "Smiles2Gromacs",
+]