  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/ .
