In this repo, we provide a set of scripts we use for the analysis of dynamic graph generated from MD (Molecular Dynamics) simulations. Here, amino acids represent nodes and edges are formed in case their distance is below a certain threshold (unit-sphere graphs). The analysis of these graphs is performed with DNA (Dynamic Network Analyzer).
The graph are read from the DNA format, each from a separate directory containing initial graph and batches.
The java code used for the execution can be found in the
The two main execution classes (
Vis.java) are all located in the package
Ant Build File
To build jars for the three main Java classes (
vis.jar), an ant build file is provided in
analysis/, we provide a set of bash scripts that can be used for performing the afforementioned analyses.
For the execution of the analysis, we use the JOBS scripts.
Performing the analyses using
Generation of animated gifs of a given graph using
Some results can be found on dynamic-networks.org.