It is wellknow that the output of an MD simulation could provide both in-breath and in-depth insights regarding the system under study. Thus, the development of advanced analysis tools to allow accurate and fast extraction of such insights is a key task to be achieved. MDAnalysis is an object-oriented toolkit to analyze MD trajectories developed since 2010 as an open source Python library by Michaud-Agrawal et al. This toolkit contains several analysis modules and given its modularity, the development of new tools is straightforward. The last decade has witnessed a growing interest in the study of the presence, absence and functional role of water on internal cavities of proteins. Despite this broad interest, the discovery, characterization and study of protein cavities filled by water, is hardly accessible by experimental techniques. As a result, MD simulations have arisen as an excellent tool to observe, with atomistic detail, the structure and dynamics of water around or inside proteins. However, no unified water-dynamics analysis tool is available to date. The current interest of our group on the use of MD simulations to study water dynamics and ordering inside Connexins hemichannels and gap-junction channels led us to develop an MDAnalysis module suitable to conduct water dynamics analyses.
Results
In this work we present a new MDAnalysis module, the WaterDynamics module, dedicated to produce analysis to understand the dynamics and ordering of water inside MD simulations. This tool is able to xtract from MD-trajectories key information about the ordering and dynamics of confined water. The WaterDynamics module allows the computation of properties such as angular probabilities (AP) for several orientational descriptors of water such as the H-H bond, the O-H bond and dipole vector, water orientational relaxation (WOR), hydrogen bond lifetimes (HBL), Mean Square Displacement (MSD) and Survival Probabilities (SP)