Mxdrfile: read and write Gromacs trajectories with Matlab

Abstract

Progress in hardware, algorithms, and force fields are pushing the scope of molecular dynamics (MD) simulations towards the length- and time scales of complex biochemical processes. This creates a need for developing advanced analysis methods tailored to the specific questions at hand. We present mxdrfile, a set of fast routines for manipulating the binary xtc and trr trajectory files formats of Gromacs, one of the most commonly used MD codes, with Matlab, a powerful and versatile language for scientific computing. The unique ability to both read and write binary trajectory files makes it possible to leverage the broad capabilities of Matlab to speed up and simplify the development of complex analysis and visualization methods. We illustrate these possibilities by implementing an alignment method for buckled surfaces, and use it to briefly dissect the curvature-dependent composition of a buckled lipid bilayer. The mxdrfile package, including the buckling example, is available as open source at http://kaplajon.github.io/mxdrfile/ .