MD Packages
- Amber costs $400 for Academic use. It does come with the source code and demos, but is only shiped via CD.
- Tinker does not seem to have a parallel implementation that I noted on the website.
- NAMD uses Charm++ for parallism. According to this post NAMD can be compiled with MPI support but runs a bit slower.
Since the primary goal of this project is:
For a very large molecule set, which may or may not be able to fit in memory on a single machine, harness parallelism to diffuse the load and incease performace. We have some prereq's for any MD module that we consider.
- Must be MPI compatable to fit with our framework (What about MP_Lite?)
- Must have a clearly specified, plain text input file formats that other modules can adapt to easily.
The goal of this post is to start the conversation about MD modules in F@C, and the requirements that new modules must adhere to in order to be classified as a potential module.
Posted by hursejo at May 12, 2004 09:22 AM