Feature Tools

ms2par

The feature tool ms2par is GUI-based and allows for a convenient generation of *.par files according to user specifications, cf. Figure. It defines the molecular model, ensemble, thermodynamic state point, time step, number of equilibration steps, etc. Furthermore, the tool proposes a cut-off radius, based on the input data. After the user completes the specifications, the program generates the ASCII file *.par, to be read by ms2.

Applying ms2par is easy and intuitive even for new users. An example for its use is given in the tutorials on this webpage.

Snapshot (click to enlarge) of ms2par generating a *.par file for a MD simulation of the pure substance cyclohexanol.

ms2par is a java application and runs independently on all operating systems.

ms2chart

ms2chart is a GUI-based java applet for evaluating the simulation results from ms2. The program plots the evolution of properties. The property shown on the different graph axes is chosen from a drop down menu. The plot is shown directly in the graphical user interface.

For a better analysis ms2chart allows various features: plotting block averages as well as simulation averages into the same plot, changing the design of the plot, individual labeling of the axes and adjusting the frame detail of the plot. All plots can be exported as in png-format. If needed, simulation details can be displayed, i.e. the simulation specifications in the *.par file as well as the results in the *.res file and the simulation summary in the *.log file.

The analysis program ms2chart can be executed at any time of the simulation, i.e. also while the simulation is still ongoing. There is no loss of data, if it is run "on the fly".

Snapshot (click to enlarge) of the tool ms2chart. The picture shows the analysis of the simulation of liquid cyclohexane.

The tool ms2chart is easy to understand and can be handled intuitively. It allows for an easy first analysis of the ms2 simulations. Advanced users will use ms2chart for a quick check of simulation results, such as whether the equilibration time was appropriate or for a fast analysis, which is important if extensive series of runs are performed.

ms2molecules

The program ms2molecules is a visualization tool for ms2. The program displays the molecular trajectories that are stored by ms2 as a series of configurations in the *.vim file.

ms2molecules visualizes molecular sites by colored spheres. The colors are user defined. The size of a sphere is by default proportional to the LJ parameter s, but can be changed manually. This feature facilitates monitoring a component of interest, by reducing the size of other components, e.g. solvents. Other features like zooming into or out of the simulation volume as well as rotating the simulation volume also facilitate the analysis of the simulation.

The visualization can be exported via snapshots in the jpg-format or as movies in the avi format.

The program is based on OpenGL and written in C. The handling of the program is simple and console based. Requirements for the program are OpenGL in a Windows or Linux environment. The figure shows a snapshot of a ternary mixture, taken with the program ms2molecules.

Snapshot (click to enlarge) of a ternary mixture taken with the visualization tool ms2molecules. The mixture consists of ethane colored red, methane colored orange, and carbon dioxide colored green. The white frame illustrates the size of the simulation box.

The program ms2molecules is convenient to gain insight into the trajectory of the system, or the state of the system, respectively.