Modar

About Modar

Modar is a software package for molecular dynamics (MD) simulation, including modeling, sampling, and result analysis. A simple and easy script language is implemented in Modar for carrying out all relevant functions needed for MD simulation. Taking the advantage of the flexibility of script language, Modar can help user realize advanced level modeling, reslult analyzing, even do some algorithm and methodology study jobs without playing with the source code. Modar is free for all academic or nonprofit research purposes.

Downloads

The prebuilt Modar binaries are deliveried in BeeMD package. For downloading please go here

Documents

• A quick guide to Modar script language
• Modar commands list
• Select expression
• Availabe ensemble and integrator combinations in Modar
• Modar MD energy profile viewer
• Energy and relevant terms reported by Modar
• Units measurement in Modar
• File types in Modar

Examples

• Example 1: Building a water box
• Example 2: PMF of displacement of ions pairs in water
• Example 3: Ion liquid simulation
• Example 4: Protein simulation in explicit solvent
• Example 5: Base flipping in RNA by Steered MD
• Example 6: Quick PMF evaluation for protein and ligand binding
• Example 7: Membrane simulation: building a lipid bilayer
• Example 8: Membrane simulation: drug molecule translocation

Run a MD job using Modar

./modar run.inp

Where “run.inp” is an input scipt file composed in Modar script language, and the log messages will be printed to a log file, which has the same file name of the input file but with a “.log”, and it will be “run.log” in this example. The timing information (how long the job will take) and the size of trajectory file will be reported on the fly on screen.

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