Week 3

So after the Streptavidin/biotin example worked, I went to prepare other examples. However, they were not working as they were supposed to. After working for a while with David we determined that the partial energies assigned by AutoDockTools were wrong. So the preparation of test cases is now postponed until we can get a license for SYBYL, which can assign the proper charges.

I investigated OPT++, which turns out to be very good. It's minimization of our energy function is faster than NAMD's. I messed with different optimizations, but the conjugate gradient one seems to be the best for our function.

After that I helped debug some of the new energy force field code, which needs to be finished before we can move on.

Week: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10