GROMACS is a Molecular Dynamics (MD) package, primarily designed to simulate biomolecules, such as proteins, lipids and nucleic acids.

A cross-platform distribution is available as an egg from EDM, currently supporting version 2019.4

Chemicals Module Design

The Force Gromacs wrapper is built on top of a small library defining a hierarchical collection of generic chemical species, force_gromacs.chemicals. It is build for extensibility, providing base traits classes as well as the interfaces for these objects that could be fulfilled by objects in an external package.

The lowest object in this hierarchy is the IParticle, which defines a very simple interface for a class that possesses both mass and charge attributes. A particle is not therefore fixed to a specific length scale since a proton, atom, molecule or large molecular complex species would all be able to fulfil this interface. An example of an object that fulfils this interface is the GromacsParticle class.

>>> my_particle = GromacsParticle(mass=12, charge=0)
>>> my_particle.mass
>>> my_particle.charge

Next up from this is the IParticleGroup class, representing a collection of particles. The interface inherits from IParticle, so that a group of particles can also be represented by a reduced representation given by a single particle.

In the atomistic length scale, we also introduce the IFragment class to describe molecular fragments. A fragment represents a part of a molecule containing a single or collection of covalently bonded particles. Therefore it inherits from IParticleGroup, but also contains the attribute stoichiometry, the stoichiometric number of each fragment in the molecule. An example of an object that fulfils this interface is the GromacsFragment class, which also contains (optional) information regarding the geometry of molecular fragments.

>>> my_fragment = GromacsFragment(particles=[my_particle])
>>> my_fragment.mass
>>> my_fragment.charge
>>> my_fragment.stoichiometry

A molecule of sodium cabonate \(Na_2CO_3\) consists of 3 fragments: two \(Na^{+}\) atomic ions and the \(CO_3^{2-}\) molecular ion:

\[Na_2CO_3 \leftrightarrow 2Na^{+} + CO_3^{2-}\]

All ionic species are free to dissociate, and therefore do not possess any constraints in a MD simulation regarding their equations of motion. We can also freely add and take away integer numbers of these objects in a simulation cell and calculate their molecular concentrations in a mixture. However, in reality we cannot ‘add’ fragments from a jar on the laboratory shelf, and instead describe formulations by their constituent molecules (typically in concentration % by mass).

Therefore, the Molecule class is designed to represent a full computational model for a chemical found in the laboratory. It contains a list of IFragment classes, and must be overall electronically neutral. We can describe the calcium carbonate molecule by the following force_gromacs objects:

Firstly the constituent atomic particles:

>>> sodium = GromacsParticle(element='Na', mass=11, charge=1)
>>> carbon = GromacsParticle(element='C', mass=12, charge=4)
>>> oxygen = GromacsParticle(element='O', mass=16, charge=-2)

Next the fragment ions:

>>> sodium_ions = GromacsFragment(particles=[sodium], stoichiometry=2)
>>> sodium_ions.mass
>>> sodium_ions.charge

>>> carbonate_ion = GromacsFragment(particles=[carbon] + 3 * [oxygen])
>>> carbonate_ion.mass
>>> carbonate_ion.charge

And finally the full molecule:

>>> sodium_carbonate = Molecule(fragments=[sodium_ions, carbonate_ion])
>>> sodium_carbonate.mass
>>> sodium_carbonate.charge
>>> sodium_carbonate.neutral