Computational methods such as molecular dynamics (MD) are now an indispensable component of modern structural biological and (bio)chemical research, as they provide researchers with details largely inaccessible to current experimental techniques. Moreover, recent hardware (e.g., GPU-based machines) and software developments have rendered computing-intensive tools, such as MD engines like NAMD, tremendously powerful allowing scientists to simulate bigger and more complex molecular systems for longer time scales. The migration of supercomputer-only calculations to more affordable and accessible machines has made MD simulations attractive to a broad community of researchers not necessarily experts in the application of these methods, creating a need for easy-to-use tools that alleviate the initial (steep) learning curve, and streamline tedious and repetitive processes while providing the user with the information necessary to make informed decisions. QwikMD, VMD’s Modeling and Simulation Setup/Analysis toolkit, allows the user to prepare MD simulations in a point-and-click fashion, using pre-set parameters to prepare unbiased, steered, MD flexible fitting (using MDFF plugin) or hybrid QM/MM simulations, while fully integrated with VMD’s molecular visualization interface. These simulations are then performed with NAMD on a local machine, on a cloud-computing facility like Amazon’s AWS, or on a supercomputer. Beyond providing assistance during the preparation, QwikMD ensures the reproducibility of the simulations by recording and logging all parameters and steps taken during the preparation and analysis process. The results of the simulations are then readily analyzed in QwikMD using a wide variety of tools available in VMD. If a molecular component of the system (e.g., a ligand) needs to be modeled, QwikMD automatically directs the user to the newly developed molecular modeling tool Molefacture, an interactive, easy-to-use interface that allows the user to quickly make modifications and assign automatically compliant atom types and parameters with the CHARMM force-field using the CGenFF program/server (cgenff.umaryland.edu). If the parameters require further refinement, Molefacture is also interconnected with VMD’s force field toolkit (ffTK) plugin, recently extended to be compatible with the ORCA quantum package. Collectively, the tool chest available in QwikMD reduces the barrier against using simulations and modeling tools, especially for novice users.

Accessible molecular modeling environment with VMD and NAMD

2019 Fall National Meeting

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