How To Do Very Large Scale Simulations
HIV-1 Capsid
It is now becoming possible to routinely perform very large (multi-million) molecular dynamics simulations using TCBG's molecular dynamics program, NAMD, and its molecular visualization program, VMD.
Such large-scale simulations can be performed using the current NAMD release, NAMD 2.9:
- NAMD 2.9 can be downloaded freely from our NAMD website
- NAMD 2.9 is also available also on most major supercomputer systems in the United States
- Particular instructions for carrying out simulations of large systems are given on the NAMD web site here
Our molecular visualization program VMD can be used to set up large system simulations and analyze the simulation results:
- VMD can be downloaded freely from our VMD website
- Extensive instructional materials on using VMD are available freely on our website here
- Particular instructions for solvating large structures are available on the VMD web site here
The utility of large simulations is exemplified by our publication in Nature:
"Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics." Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang. Nature, 497:643-646, 2013.
The paper describes a 100 nanosecond trajectory of a 64 million atom structure of an HIV capsid. On our HIV website one can find more information on the system, including instructions on how to download and visualize the HIV trajectory, which we have made publicly available, utilizing VMD.
Large-scale simulations are not the niche purview of computational groups such as our own. For example, Jason Roberts, an experimental immunologist in Australia, successfully performed multi-million atom NAMD simulations on viruses.
