07 July 2016 4 6K Report

I've been data-mining and I can't find anything lately along the lines of my questions. I've noticed that a lot of researchers like to do their molecular dynamics simulations with AMBER and then use VMD for visualization of the final states. But I know for a fact that VMD is capable of accomplishing many solvation simulations, multi-sequence analysis, rmsd plotting, and free-energy calculations (accounting entropy and enthalpy). I could try the modules with a shot in the dark, and I've looked at many tutorials, but I just want some research to go off of so I can look at the physical assumptions and techniques. 

If it's not too much trouble could you link me some in-silico thermodynamics studies? 

Thanks.

-Adron 

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