Last November I wrote a molecular simulator called Go Replicants! that uses Go potentials to simulate protein folding processes and study some of their thermodynamic properties. Its source code and some instructions can be found here.
My goals while writing the program were manifold (pun intended):
- First and foremost, I wanted to understand the simulation techniques used by a research group that I collaborate with. Among these are parallel tempering (a.k.a. replica exchange) Monte Carlo, WHAM, etc.
- I was also looking forward to learning OpenMP and the GNU Scientific Library for quite some time, so this gave me the perfect opportunity to do so.
- Many projects have been migrating from GNU autotools to CMake. I was curious about it and wanted to become acquainted with CMake too.
The code can still be improved upon, of course. But besides cleanups or feature additions, and considering that my new toycomputer at work has two NVIDIA Tesla M2050s, I think the next step is to develop GPU capabilities.
Oh, I almost forgot that its Git repository is cloned at Github.
