jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability.

Molecular dynamics (MD) is a technique to simulate movements of molecular structures to understand their functional behavior. GROMACS is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. This makes it powerful but also complicated to handle. We introduce jSimMacs, a Java application for creating molecular dynamics projects in GROMACS. It simplifies the handling of files and options via an intuitive user interface. Users unexperienced in MD can work along prepared lines, while experts may enjoy a significant relief from the tedium of typing and scripting. Furthermore, jSimMacs supports 3D interactivity and the launch of remote projects on other computers accessible via networks. Thus, jSimMacs not only opens GROMACS to a broader public but also eases the burden of performing series of MD runs, as necessary in parameter studies.