Leveraging molecular dynamics data with Sims

A Sim is a Treant with specialized components for working with molecular dynamics data. In particular, it can store a definition for an MDAnalysis Universe for painless recall, as well as custom atom selections.


Since Sims are Treants, everything that applies to Treants applies to Sims as well. See the datreant documentation for how Treants work and effectively used.

As with a normal Treant, to generate a Sim from scratch, we need only give it a name

>>> from mdsynthesis import Sim
>>> s = Sim('adk')
>>> s
<Sim: 'adk'>

And we can immediately give the Sim characteristics like tags:

>>> s.tags.add('biased', 'closed-to-open', 'mep')
>>> s.tags
<Tags(['biased', 'closed-to-open', 'MEP'])>

and categories:

>>> s.categories['sampling method'] = 'DIMS'
>>> s.categories['sampling '] = 'heavy atom'
<Categories({'sampling ': 'heavy atom', 'sampling method': 'DIMS'})>

These can be used later to filter and aggregate Sims when we have many to work with. They can also be used as switches for analysis code, since we may need to do different things depending on, for example, the type of sampling method used to produce the trajectory.

Defining the Universe

What makes a Sim different from a basic Treant is that it can store an MDAnalysis Universe definition. We can access the Sim’s Universe directly with:

>>> s.universe

At this point, we get back None. However, we can define the Sim’s Universe by giving it one direclty:

>>> import MDAnalysis as mda
>>> s.universe = mda.Universe('path/to/topology.psf',
>>> s.universe
<Universe with 3341 atoms and 3365 bonds>

The Universe definition is persistent, so we can get back an identical Universe later from another Python session with our Sim:

>>> import mdsynthesis as mds
>>> s = mds.Sim('adk')
>>> s.universe
<Universe with 3341 atoms and 3365 bonds>

Changing the Universe definition


This interface may be removed in a future release, but remains for now due to limitations in MDAnalysis. It is encouraged to set the Universe definition directly as shown above.

We can directly change the topology used for the Sim’s Universe with

>>> s.universedef.topology = 'path/to/another/topology.psf'

then we get back a Universe built with this topology instead:

>>> s.universe.filename

We can also change the trajectory:

>>> s.universedef.trajectory = 'path/to/another/trajectory.dcd'

which re-initializes the Universe with both the defined topology and trajectory:

>>> s.universe.trajectory
<DCDReader /home/bob/research/path/to/another/trajectory.dcd with 98 frames of 3341 atoms>

We can also define our Universe as having multiple trajectories by giving a list of filepaths instead. Internally, the Universe generated will use the MDAnalysis ChainReader for treating the trajectories as a contiguous whole.


Changing the topology or trajectory definition will reload the Universe automatically. This means that any AtomGroups you are working with will not point to the new Universe, but perhaps the old one, so it’s generally best to regenerate them manually.

Storing keyword arguments

If the Universe needed requires keyword arguments on initialization, these can be stored as well. For example, if our topology was a PDB file and we wanted bonds to be guessed upfront, we could make this happen every time:

>>> s.universedef.kwargs = {'guess_bonds': True}

Reinitializing the Universe

If you make modifications to the Universe but you want to restore the original from its definition, you can force it to reload with:

>>> s.universedef.reload()

API Reference: UniverseDefinition

See the UniverseDefinition API reference for more details.

Storing custom atom selections

MDAnalysis includes its own selection language for extracting AtomGroup objects, which function as ordered lists of (selected) atoms from the system. The selection strings needed to specify these can be long and complex, and sometimes multiple selection strings are required in a particular order to extract a given AtomGroup from all the atoms in the Universe. Moreover, given different simulation systems, the same selection of atoms (e.g. the “solvent”) might require a different set of selection strings.

Fortunately, Sims provide a mechanism for storing (many) atom selections. Say we want to select the LID, CORE, and NMP domains of adenylate kinase, the protein we simulated. We can store these immediately:

>>> s.atomselections['lid'] = 'resid 122:159'
>>> s.atomselections['nmp'] = 'resid 30:59'
>>> s.atomselections['core'] = ('resid 1:29', 'resid 60:121', 'resid 160:214')

We can now get new AtomGroups back for each selection at any time with the create() method:

>>> s.atomselections.create('lid')
<AtomGroup with 598 atoms>

>>> s.atomselections.create('core')
<AtomGroup with 2306 atoms>

and we don’t have to remember or know how ‘lid’ or ‘core’ are defined for this particular system. If we have other simulations of adenylate kinase performed with other molecular dynamics engines or with different forcefields, we can store the atom selection strings required for those systems in the same way, perhaps using the same names ‘lid’, ‘core’, etc. This abstraction allows us to work with many variants of a simulation system without having to micromanage.


Storing a list of strings as a selection will apply them in order, producing an AtomGroup concatenated from each one in the same way as providing multiple strings to select_atoms() does. This is especially useful when storing selections used for structural alignments.

Want just the selection strings back? We can use get():

>>> s.atomselections.get('lid')
'resid 122:159'

# or using getitem syntax
>>> s.atomselections['lid']
'resid 122:159'

Atom selections from atom indices

Do you already have an AtomGroup and prefer to define it according to its atom indices instead of as a selection string? That can be done, too:

>>> lid = s.universe.select_atoms('resid 122:159')
>>> s.atomselections['lid'] = lid.indices
>>> s.atomselections.create('lid')
<AtomGroup with 598 atoms>

Lists/tuples of selection strings or atom indices can be stored in any combination as a selection. These are applied in order to yield the AtomGroup when calling the create() method.

API Reference: AtomSelections

See the AtomSelections API reference for more details.

API Reference: Sim

See the Sim API reference for more details.