mosdef
MoSDeF Workshop¶
This workshop will present MoSDeF [1], a suite of extensible Python tools designed to facilitate topology initialization and atom-typing for molecular dynamics and Monte Carlo simulations in a way that is programmatic, extensible, and reproducible.
MoSDeF is designed around three key pieces of software, mBuild [2,3], Foyer [4,5] and GMSO. mBuild is a topology construction tool where interchangeable compounds are programmatically connected in a hierarchal manner. This allows for construction of systems ranging in complexity. Examples of producible topologies include liquid mixtures, homo-and co-polymers, slits, pores and nanotubes, crystalline solids, functionalized surfaces and more.
Foyer is a general tool for applying force fields to molecular systems (i.e., atom-typing) that does not rely upon rigid rule hierarchies or force field model specific atom types. Using SMARTS strings, foyer atom types topologies through a graph-matching algorithm, which lowers barriers to customizing, and extending force fields. Additionally, SMARTS strings are both human and machine readable, making it easier disseminate both the atom-typing logic and parameters used in a force field.
GMSO (General Molecular Simulation Object) [7], is a software tool that provides the flexible data structure needed to store, manage, and manipulate chemical topology parameters. GMSO uses the sympy library to represent molecular modelling potentials, and their parameters, as algebraic expressions. This flexibility allows GMSO to easily support a wide range of interaction potentials beyond commonly used forms. Using GMSO’s xml-file schema, force field specification (and atom-typing through foyer) is handled the same way for atomistic and coarse-grain systems.
MoSDeF can output fully parameterized structures to various file formats used by common simulation engines (e.g. GROMACS, LAMMPS, HOOMD-Blue, GOMC, Cassandra). Using a well-defined Python API, MoSDeF reduces the reliance on traditional input files with strict syntax requirements. As such, MoSDeF provides a flexible, programmatic, yet clear approach to encapsulate the routines and parameters used when initializing and performing molecular simulations, which increases transparency and reproducibility of simulation results.
[1] https://github.com/mosdef-hub
[2] C. Klein, J. Sallai, T. J. Jones, C. R. Iacovella, C. McCabe, and P. T. Cummings, “A Hierarchical, Component Based Approach to Screening
Properties of Soft Matter,” in Foundations of Molecular Modeling and Simulation, 2016, pp. 79-92. [3] https://github.com/mosdef-hub/mbuild
[4] Iacovella, C. R.; Sallai, J.; Klein, C.; Ma, T. In Idea Paper: Development of a Software Framework for Formalizing Forcefield Atom-Typing for Molecular Simulation, 4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4), 2016. [5] https://github.com/mosdef-hub/foyer [6] http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html [7] https://github.com/mosdef-hub/gmso