createsys: Create molecular systems for QM/MM hyperreactor dynamics

This package bundles some utilities for the fast setup of QM/MM hyperreactor simulations run with the adaptive_sampling package. At some point, these packages might be merged.

Available features

• intial conformation generation of a mixture of reactants in a sphere sourrounded by a cubical box of solvent molecules (by accessing packmol through a simple wrapper). For each molecule, a single .pdb is required.

• equilibration routines based on openmm/adaptive_sampling:

  • energy minimization

  • multi-step warmup MD

  • Box equilibration MD with Monte-Carlo-Barostat

Note

A spherical confinement can be added to equilibration MDs to keep the reactants centered.

• automated force field setup based on a single .pdb. With geometry-inferred bond orders, an openff-SMIRNOFF-based force field (openff-2.2.1.offxml) is created together with a suitable topology. This function prioritizes convenience over customizability.

Examples

For initial configuration generation of a non-enzymatic nucleoside synthesis example, see here.

Equilibration routines are found here.

For the topology and force field generation, simply use

from createsys import createTopologyAndForceFieldFromPDB

topology, forcefield = createTopologyAndForceFieldFromPDB("mystructure.pdb")

The connectivity information of the PDB is used to determine molecular connectivity. Please note that bond orders are inferred from the geometry.

To identify the inner region of a structure created with createsys, you can use

from createsys import getAtomIndicesFromResidueNames
atom_indices_inner_sphere = getAtomIndicesFromResidueNames("mystructure.pdb", ["INN"])

Installation

As this package is an add-on to the adaptive_sampling package, please follow the instructions given here. This also installs createsys.