The rest of the past week has been pretty slow. The PI and a good portion of the lab have been out of town for a meeting. As such, the lab has largely shut down. The results of my MD (molecular dynamics) simulation are in, though, and I'm glad to say nothing looks too messed up. I had time to do an initial analysis, which seemed to show that both simulations I had ran were moving towards the active conformation, which is very good news. The analysis also showed, however, that neither system was fully equilibrated. Because I need a fully equilibriated system to be able to draw real conclusions from the data, I ran the same simulations again, but this time for 2.5x longer. This should be long enough for the system to equilibrate completely.
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