(161d) Efficient Trajectory Analysis Using Selection Tools in Gromacs

Authors: 
Brian, J. P., University of Louisville
Jaeger, V., University of Louisville
The GROMACS select command provides the capability to mine data from trajectories in very powerful ways, especially using the dynamic selection option. However, there is a dearth of information regarding complex program syntax. Program documentation lacks any examples beyond very simple statements. Moreover, error reporting is completely uninformative, complicating its adoption by novice users. Drawing upon prior knowledge and experience with SQL, we have deciphered the GROMACS syntax peculiarities. An example of practical, high throughput, data analysis covering millions of simulation frames will be demonstrated. We foresee useful applications of the select command in analyzing solvent-solute interactions, lipid bilayer structures, and the evolution of large structural changes in biomolecular systems. The program allows for simplification of the treatment of periodic boundaries, thus eliminating certain pre-processing steps in data analysis. We have recently integrated the select command with other trajectory analysis tools. The command now more seamlessly interfaces with other GROMACS analysis tools, allowing users to mine data that were previously computationally expensive or required external programs. A new tutorial for the implementation of this powerful tool and its applications has been developed to help novice users become masters.