Week 1

Houston summer has arrived, and for those of you who don't know that means that it's hot. Good thing the lab that I work in is set to a below freezing temperature. Last summer I implemented code that calculated the CHARMM force field for a given molecule. This year the first goal was to add solvation terms, cutoffs and optimize the code. I spent quite a bit of time reading about ways to calculate the contribution to the energy from the solvent. The generalized born model seemed to be one of the more popular ones, so I started implementing it. I ran into some problems as the born radii I was getting were wrong. However, we discovered that CHARMM isn't the best force field to use for docking. Other energy functions that might be better incorporate the solvent energies into their parameters and so they do not have an explict solvent term. I put that aside and started working on cutoffs for non bonded interactions. I used the By-Clusters-in-Cubes algorithm (Petrella R.J., Andricioael I., Brooks B.R., Karplus M J Comp Chem 24: 222-231, 2003). See next week for more exciting developments in cutoffs!

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