Molecular Simulation - Analysis

How we preformed MD simulations

• Create a standard folder structure.

• Setting up the configuration: 1ns, 300k temperature, minimization step - 2000.

• Run MD simulation using NAMD2 tool.

• Visualize the results using VMD.

• Extract Salt bridges data.

• Store this data into DB using python script.

Benchmark Tool

Utilizing SYSBENCH

1. Evaluate the performance of the Database.

2. Allows us to compare and Optimize the database.

3. Sysbench is open source-performance testing tool.

4. It Offers flexibility, configurability and detailed reporting.