MDAnalysis is a free and open source Python framework built to analyze molecular dynamics trajectories generated by Charmm, NAMD, or LAMMPS.
MDAnalysis allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides an extremely flexible and relatively fast framework for complex analysis tasks.
In addition, Charmm-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.
Detailed instructions on how to install and use the MDAnalysis utility on your Mac are available HERE.
What's New in This Release: [ read full changelog ]
· multithreaded distance_array() (Issue 80, experimental); see the new core.parallel.distance module
· MDAnalysis.analysis.rms for simple RMSD analysis
· format of input coordinates can be set as (filename, format) tuples (Issue 76)
· new AtomGroup.asphericity() and AtomGroup.shapeParameter() methods to compute shape descriptors.
· access to forces (AtomGroup.forces with get_forces() and set_forces(); the default unit for force is kJ/(mol*A) and it is automatically converted from/to native). Currently, only the TRR Reader/Writer support forces.
· all element masses
· logger reports current version when starting
· fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
· fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
· fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
· fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
· fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
· Issue 12...