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
@Jun Zhang: you're comparing apples to oranges: VMD is a visualization program, while NAMD is the molecular dynamics engine. NAMD is certainly as "reliable" as other MD codes such as AMBER, GROMACS and CHARMM. The biggest problem is probably in the force field, but NAMD can use all three force-fields (CHARMM, GROMACS and AMBER).
Entropy: A concept that is not a physical quantity
https://www.researchgate.net/publication/230554936_Entropy_A_concept_that_is_not_a_physical_quantity
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