Jack

Sorry for not posting, but my week's been kind of crazy. Basically, we finally ran full simulations of my system, and while they went well, the program that I had learned to use proved far to inefficient. Even with 64 cores working, I was only getting about 1ps a day, and I need 100ps, give or take, to have any sort of reasonable certainty that my system is stabilized. Since I don't want to be here till November, we've decided to switch to a new, more efficient program called NAMD. The bad news is that most of my old simulations are now fairly useless. The good news is that NAMD is fairly similar in terms of usage to amber, and most of the preparatory work I did is still valid. Since I am also going to be using Calhoun (our supercomputer) for all the simulations, this time around should be much quicker. At the moment I'm working on a ion bunching problem which we had encountered early with amber and which we had fixed. Unfortunately, that fix, for convoluted reasons, didn't carry over the NAMD, so no I have to re-fix it. Luckily, this time I know how.
Jack