StreaMD: Advanced analysis of molecular dynamics using R.
Maximilian J Dombrowsky, Sven Jager, Benjamin Schiller, Benjamin E Mayer, Sebastian Stammler, Kay Hamacher
Author Information
- Maximilian J Dombrowsky: Computational Biology and Simulation, Department of Biology, TU Darmstadt, Germany.
- Sven Jager: Computational Biology and Simulation, Department of Biology, TU Darmstadt, Germany. ORCID
- Benjamin Schiller: Privacy and Data Security, Department of Computer Science, TU Dresden, Germany.
- Benjamin E Mayer: Computational Biology and Simulation, Department of Biology, TU Darmstadt, Germany.
- Sebastian Stammler: Computational Biology and Simulation, Department of Biology, TU Darmstadt, Germany.
- Kay Hamacher: Computational Biology and Simulation, Department of Biology, TU Darmstadt, Germany.
Gromacs is one of the most popular molecular simulation suites currently available. In this contribution we present streaMD, the first interface between Gromacs trajectory files and the statistical language R. The amount of data created due to ever increasing computational power renders fast and efficient analysis of trajectories into a challenge. Especially as standard approaches such as root-mean square fluctuations and the like provide only limited physical insight. In our streaMD package integration of the Gromacs I/O libraries with advanced, graph-based analysis methods as the java library Stream leads to both: improved speed and analysis depth. We benchmark our results and highlight the applicability of the package by an interesting problem in RNA design, namely the interaction of tetracycline with an aptamer. © 2018 Wiley Periodicals, Inc.
