Highlights of our Work
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made with VMD
Everything that living things do can be understood in terms of jigglings and wigglings of atoms.Richard Feynman's remark in the early 1960's summarizes what is today widely accepted, namely, that molecular processes can be described by the dynamics of biological molecules, therefore connecting protein dynamics to biological function. Molecular dynamics (MD) is by far the best tool to investigate
wigglingsof biological systems. Advances in both software and hardware have spread the use of MD, however the steepness of the learning curve of the methodology of MD remains high. To assist new users in overcoming the initial barrier to use MD software, and to help the more advanced users to speed up tedious steps, we have developed the QwikMD software, as decribed in a recent paper. By incorporating an easy-to-use point-and-click user interface that connects the widely used molecular graphics program VMD with the powerful MD program NAMD, QwikMD allows its users to prepare both basic and advanced MD simulations in just a few minutes. At the same time, QwikMD keeps track of every step performed during the preparation of the simulation, allowing easy reproducibility and shareability of protocols. More information about QwikMD, as well as introductory tutorials are available on our QwikMD webpage. QwikMD is available in VMD 1.9.3 or later versions.