MDTraj HDF5 Format Specification

Overview

This is the specification for a molecular dynamics trajectory file format based on HDF5 which is supported by the MDTraj package.

Why HDF5?

Design Goals

In storing MD trajectory data for the for purposes including very large scale analysis, there are a few design goals. (1) The trajectories should be small and space efficient on disk. (2) The trajectories should be fast to write and fast to read. (3) The data format should support flexible read options. For instance, random access to different frames in the trajectory should be possible. It should be possible to easily query the dimensions of the trajectory (n_frames, n_atoms, etc) without loading the file into memory. It should be possible to load only every n-th frame, or to directly only a subset of the atoms with limited memory overhead. (5) The trajectory format should be easily extensible in a backward compatible manner. For instance, it should be possible to add new arrays/fields like the potential energy or the topology without breaking backwards compatibility.

Other Formats

Currently, MDTraj is able to read and write trajectories in DCD, XTC, TRR, BINPOS, and AMBER NetCDF formats, in addition to HDF5. This presents an opportunity to compare these formats and see how they fit our design goals. The most space efficient is XTC, because it uses 16 bit fixed precision encoding. For some reason, the XTC read times are quite slow though. DCD is fast to read and write, but relatively inflexible. NetCDF is fast and flexible. BINPOS and MDCRD are garbage – they’re neither fast, small, nor flexible.

What’s lacking?

Of the formats we currently have, AMBER NetCDF is the best, in that it it satisfies all of the design goals except for the first. But the trajectories are twice as big on disk as XTC, which is really quite unfortunate. For dealing with large data sets, size matters. So let’s define a HDF5 standard that has the benefits of AMBER NetCDF and the benefits of XTC mixed together. We’ll use an extensible data format (HDF5), we’ll provide options for lossy and lossless compression, and we’ll store the topology inside the trajectory, so that a single trajectory file always contains the information needed to understand (and visualize) the system.

Details

This specification is heavily influenced by the AMBER NetCDF standard. Significant portions of the text are copied verbatim.

Encoding

  • Files will be encoded in HDF5, a data model, library, and file format for storing and managing data produced at NCSA.
  • Arrays may be encoded with zlib compression.
  • Libraries implementing this standard may, at their desecration, round the data to an appropriate number of significant digits, which can significantly enhance zlib compression ratios.

Global Attributes

  • Conventions (required) Contents of this attribute are a comma or space delimited list of tokens representing all of the conventions to which the file conforms. Creators shall include the string Pande as one of the tokens in this list. In the usual case, where the file conforms only to this convention, the value of the attribute will simply be ``Pande’‘. Readers may fail if this attribute is not present or none of the tokens in the list are Pande. Optionally, if the reader does not expect HDF5 files other than those conforming to the Pande convention, it may emit a warning and attempt to read the file even when the Conventions attribute is missing.
  • ConventionVersion (required) Contents are a string representation of the version number of this convention. Future revisions of this convention having the same version number may include definitions of additional variables, dimensions or attributes, but are guaranteed to have no incompatible changes to variables, dimensions or attributes specified in previous revisions. Creators shall set this attribute to “1.1”. If this attribute is present and has a value other than “1.1”, readers may fail or may emit a warning and continue. It is expected that the version of this convention will change rarely, if ever.
  • application (optional) If the creator is part of a suite of programs or modules, this attribute shall be set to the name of the suite.
  • program (required) Creators shall set this attribute to the name of the creating program or module.
  • programVersion (required) Creators shall set this attribute to the preferred textual formatting of the current version number of the creating program or module.
  • title (optional) Creators may set use this attribute to represent a user-defined title for the data represented in the file. Absence of a title may be indicated by omitting the attribute or by including it with an empty string value.
  • randomState (optional), ASCII-encoded string Creators may optionally describe the state of their internal random number generators at the start of their simulation. The semantics of this string are specific to the MD code and are not specified by this standard.
  • forcefield (optional), ASCII-encoded string For data from a molecular dynamics simulation, creators may optionally describe the Hamiltonian used. This should be a short, human readable string, like “AMBER99sbildn”.
  • reference (optional), ASCII-encoded string Creators may optionally specify published a reference that documents the program or parameters used to generate the data. The reference should be listed in a simple, human readable format. Multiple references may be listed simply by separating the references with a human readable delimiter within the string, like a newline.

Arrays

  • coordinates (required) shape=(n_frames, n_atoms, 3), type=Float32, units=”nanometers”. This variable shall contain the Cartesian coordinates of the specified particle for the specified.
  • time (optional), shape=(n_frames), dtype=Float32, units=”picoseconds” When coordinates on the frame dimension have a temporal sequence (e.g. they form a molecular dynamics trajectory), creators shall define this dimension and write a float for each frame coordinate representing the simulated time value in picoseconds associated with the frame. Time zero is arbitrary, but typically will correspond to the start of the simulation. When the file stores a collection of conformations having no temporal sequence, creators shall omit this variable.
  • cell_lengths (optional), shape=(n_frames, 3, 3), dtype=Float32, units=”nanometers” When the data in the coordinates variable come from a simulation with periodic boundaries, creators shall include this variable. his variable shall represent the lengths (a,b,c) of the unit cell for each frame. The edge with length a lies along the x axis; the edge with length b lies in the x-y plane. The origin (point of invariance under scaling) of the unit cell is defined as (0,0,0). If the simulation has one or two dimensional periodicity, then the length(s) corresponding to spatial dimensions in which there is no periodicity shall be set to zero.
  • cell_angles shape=(n_frames, 3, 3), dtype=Float32, units=”degrees” Creators shall include this variable if and only if they include the cell_lengths variable. This variable shall represent the angles (, , ) defining the unit cell for each frame. defines the angle between the b and c vectors, defines the angle between the a and c vectors and defines the angle between the a and b vectors. Angles that are undefined due to less than three dimensional periodicity shall be set to zero.
  • velocities (optional), shape=(n_frames, n_atoms, 3), type=Float32, units=”nanometers/picosecond” When the velocities variable is present, it shall represent the cartesian components of the velocity for the specified particle and frame. It is recognized that due to the nature of commonly used integrators in molecular dynamics, it may not be possible for the creator to write a set of velocities corresponding to exactly the same point in time as defined by the time variable and represented in the coordinates variable. In such cases, the creator shall write a set of velocities from the nearest point in time to that represented by the specified frame.
  • kineticEnergy (optional), shape=(n_frames), type=Float32, units=”kJ/mol” Creators may optionally specify the kinetic energy of the system at each frame.
  • potentialEnergy (optional), shape=(n_frames), type=Float32, units=”kJ/mol” Creators may optionally specify the potential energy of the system at each frame.
  • temperature (optional), shape=(n_frames), type=Float32, units=”Kelvin” Creators may optionally specify the temperature of the system at each frame.
  • lambda (optional), shape=(n_frames), type=Floa32 units=”“ For describing an alchemical free energy simulation, a creator may optionally notate each frame in the simulation with a value of lambda.
  • constraints (optional), shape=(n_constraints, 3), type=CompoundType(int, int, float) units=[None, None, “nanometers”] Creators may optionally describe any constraints applied to the bond lengths. constraints shall be a compound-type table (referred to a table as opposed to an array in the pytables documentation), such that the first two entries are the indices of the two atoms involved in the constant, and the final entry is the distance those atoms are constrained to.
  • topology (optional, but highly recommended), shape=(1, length_as_needed) type=string For protein systems, creators shall describe the topology of the system in ASCII encoded JSON. The format for the topology definition is described in the topology subsection of this document. The JSON string encoding the topology shall be stored as the sole row in an array of strings.

Array Metadata

  • For arrays that contain naturally unitted numbers (which is all of them except for ‘topology’), creators shall explicitly declare their units. The unit system of length=nanometers, time=picoseconds, mass=daltons, temperature=Kelvin, energy=kJ/mol, force=kJ/mol/nm shall be used everywhere. For angles, degrees shall be used. The units shall be set as an “attribute”, on the array, under the key “units”, within the parlance of HDF5. It shall be a string.
  • For arrays that contain numbers which have been rounded to a certain number of significant digits, creators shall declare the number of significant digits by setting the “least_significant_digit” attribue, which should be a positive integer.

Extended Arrays

Creators may extend this format by adding new arrays. Arrays containing per-atom and per-frame data that naturally possesses physical units should declare those units explicitly in the array attributes. Readers should be flexible, ignoring the presence of arrays that they are not equiped to handle.

Topology

Rational

It is our experience that not having the topology stored in the same file as the the trajectory’s coordinate data is a pain – it’s just really inconvenient. And generally, the trajectories are long enough that it doesn’t take up much incremental storage space to store the topology in there too. The topology is not that complicated.

Format

The topology will be stored in JSON. The JSON will then be serialized as a string and stored in the HDF5 file with an ASCII encoding.

The topology stores a hierarchical description of the chains, residues, and atoms in the system. Each chain is associated with an index and a list of residues. Each residue is associated with a name, an index, a resSeq index (not zero-indexed), and a list of atoms. Each atom is associated with a name, an element, and an index. All of the indicies should be zero-based.

The name of a residue is not strictly proscribed, but should generally follow PDB 3.0 nomenclature. The element of an atom shall be one of the one or two letter element abbreviations from the periodic table. The name of an atom shall indicate some information about the type of the atom beyond just its element, such as ‘CA’ for the alpha carbom, ‘HG’ for a gamma hydrogen, etc. This format does not specify exactly what atom names are allowed – creators should follow the conventions from the forcefield they are using.

In addition to the chains, the topology shall also contain a list of the bonds. The bonds shall be a list of length-2 lists of integers, where the integers refer to the index of the two atoms that are bonded.

Example

The following shows the topology of alanine dipeptide in this format. Since it’s JSON, the whitespace is optional and just for readability.

{'bonds': [[4, 1],
           [4, 5],
           [1, 0],
           [1, 2],
           [1, 3],
           [4, 6],
           [14, 8],
           [14, 15],
           [8, 10],
           [8, 9],
           [8, 6],
           [10, 11],
           [10, 12],
           [10, 13],
           [7, 6],
           [14, 16],
           [18, 19],
           [18, 20],
           [18, 21],
           [18, 16],
           [17, 16]],
 'chains': [{'index': 0,
             'residues': [{'atoms': [{'element': 'H',
                                      'index': 0,
                                      'name': 'H1'},
                                     {'element': 'C',
                                      'index': 1,
                                      'name': 'CH3'},
                                     {'element': 'H',
                                      'index': 2,
                                      'name': 'H2'},
                                     {'element': 'H',
                                      'index': 3,
                                      'name': 'H3'},
                                     {'element': 'C',
                                      'index': 4,
                                      'name': 'C'},
                                     {'element': 'O',
                                      'index': 5,
                                      'name': 'O'}],
                           'index': 0,
                           'resSeq': 1,
                           'name': 'ACE'},
                          {'atoms': [{'element': 'N',
                                      'index': 6,
                                      'name': 'N'},
                                     {'element': 'H',
                                      'index': 7,
                                      'name': 'H'},
                                     {'element': 'C',
                                      'index': 8,
                                      'name': 'CA'},
                                     {'element': 'H',
                                      'index': 9,
                                      'name': 'HA'},
                                     {'element': 'C',
                                      'index': 10,
                                      'name': 'CB'},
                                     {'element': 'H',
                                      'index': 11,
                                      'name': 'HB1'},
                                     {'element': 'H',
                                      'index': 12,
                                      'name': 'HB2'},
                                     {'element': 'H',
                                      'index': 13,
                                      'name': 'HB3'},
                                     {'element': 'C',
                                      'index': 14,
                                      'name': 'C'},
                                     {'element': 'O',
                                      'index': 15,
                                      'name': 'O'}],
                           'index': 1,
                           'resSeq': 2,
                           'name': 'ALA'},
                          {'atoms': [{'element': 'N',
                                      'index': 16,
                                      'name': 'N'},
                                     {'element': 'H',
                                      'index': 17,
                                      'name': 'H'},
                                     {'element': 'C',
                                      'index': 18,
                                      'name': 'C'},
                                     {'element': 'H',
                                      'index': 19,
                                      'name': 'H1'},
                                     {'element': 'H',
                                      'index': 20,
                                      'name': 'H2'},
                                     {'element': 'H',
                                      'index': 21,
                                      'name': 'H3'}],
                           'index': 2,
                           'resSeq': 3,
                           'name': 'NME'}]}]}
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