AQUA-DUCT is a new tool facilitating analysis of the flow of solvent molecules in molecular dynamic simulations. AQUA-DUCT allows extraction, analysis and visualization of the behaviour of solvent molecules during the entire simulation. Such analysis can be useful for analysis of the enzymes with the buried active site, connected with surrounding solvent by tunnels. The water flow can be controlled by molecular properties of amino acids constituting tunnels or in more sophisticated enzymes by gates controlling the opening and closing of the access pathways.
An example of AQUA-DUCT results. Approximated trajectories of all water molecules detected in active site cavity during MD simulations of M. musculus epoxide hydrolase.
The AQUA-DUCT development was supported by National Science Centre, Poland, DEC-2013/10/E/NZ1/00649