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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
jigglings
and wigglings
of 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.