Treffer: TrajectoryMergeAssist: A Python based utility to simplify extended molecular dynamics simulations on Desmond

Bioinformatics Lab, Dept. of Biotechnology, Heritage Institute of Technology, Kolkata, India Summary Working with trajectories generated with the Desmond molecular dynamics (MD) software can become quite inconvenient when simulations are extended multiple number of times with the same. Extended simulations allow Bioinformaticians to observe and interpret plots up to greater lengths of time and also do it at their own time of convenience when with lesser resources. To make this process simpler and easier, TrajectoryMergeAssist was created. It is a very handy and user-friendly GUI tool for Bioinformaticians to manage extended trajectories and finally merge all of them into a single trajectory with a series of steps and observations: With every gradual extended simulation, the user would like to view the resultant statistical plots starting from the first trajectory until the end of the second. The user would be eager to view the statistics of the same after the end of each extended simulation and that is when this tool becomes very useful. With further extended simulations, the user can use the combined trajectory obtained previously and merge it with the third and so on. The tool has been written in Python 2.7 and makes use of Tkinter, one of Python's own GUI programming toolkits. Another version has also been written in Python 3. Key Features Works with both the latest and older versions of Desmond Starting with Desmond 2018.1, a new Desmond script has been introduced and the earlier one has been deprecated for merging trajectories. TrajectoryMergeAssist checks for the same and proceeds accordingly, in order to support both the latest and earlier versions. Generates "-out.cms" file ready for use in Maestro Unlike versions prior to 2018.1, Desmond creates "merged.cms" files instead of "merged-out.cms", making it a requirement to manually rename it to the latter to make it ready for viewing on Maestro. TrajectoryMergeAssist also takes care of this by generating an "-out.cms" file instead of ".cms". Usage To be ...