The relationship between structure and function of proteins is directly connected to atomistic aspects of protein dynamics. As a major methodology in structural biology, molecular dynamics (MD) simulations permit the exploration of the physical mechanism underlying the function of proteins by examining their dynamical behavior.
To assist non-expert users and any novice to MD to overcome the initial learning curve barrier of MD simulation software, we developed QwikMD, a software that connects the widely employed and user-friendly molecular graphics program VMD to the widely adopted MD program NAMD.
Employing QwikMD, a user is able to setup an MD simulation in just a few minutes, allowing quick studies of point mutations, partial deletions and even atomic force microscopy experiments.
QwikMD provides a robust and easy-to-use environment for non-expert users in the Molecular Dynamics (MD) field. The long history of software and hardware development made MD simulations become a routine technique like any other routine laboratory technique, something that should be an easy-to-use laboratory kit.
QwikMD offers VMD style menus that carry out the series of procedures to set up, execute, and analyze MD simulations.
Far from being just a black box, QwikMD provides a user with all the underlying structures and configuration files and gives the user the opportunity to adjust them in order to specify advanced simulations.
Learn and Simulate
QwikMD facilitates for a new user the performance of MD simulations, while it also serves as a guided learning tool. Many "info buttons" provide the theoretical background of the underlying procedures carried out.
Each "info button" generates a window where the user can find fundamental information related to MD Simulations, such as the description of solvent models and protein structure, as well as short explanations of the options available in QwikMD GUI and the actions triggered by the buttons. For more information, the user is redirected to web-pages through links present in the bottom of the information window.
Live Simulation and Analysis
To perform MD simulations QwikMD takes advantage of the widely used program NAMD. In QwikMD, simulations can be either run interactively (Live Simulation option) with live view or in batch mode on a desktop computer or laptop. In Live Simulation Mode, QwikMD provides a progress bar, which helps the user to estimate the time till simulation completion.
Either during a "Live Simulation" or after a batch mode simulation, QwikMD offers the user commonly trajectory analysis employed as an initial check of the MD simulation, such as a check of root mean square deviation (RMSD) and energetic data.
