[gmx-developers] The insights into Hamiltonian's Meaning

Noel Carrascal noelcjr at hotmail.com
Thu Mar 5 16:47:05 CET 2015

David and Berk wrote:>I have been thinking a bit about these things lately and come to the >following (preliminary) conclusion:>In general, any method that replaces part of the potential by an >averaged force, like an implicit solvent model, or a coarse grained >model, uses an ill-defined Hamiltonian. Ill-defined since it contains in >part the entropic effect of the part left out. That means time becomes >meaningless, and one is not sampling a Boltzmann energy surface anymore. >Not sure if RF falls in this category too, but I think so.>I wouldn't agree with this. The Hamiltonian is well defined and you do >sample a Boltzmann distribution. But the Hamiltonian and distribution >might be very different from the "correct" Hamiltonian. GB and RF are >effective free-energies, as averaged over certain conditions. If the >conditions you use them in are different from the conditions used to >derive the potential (free-energy), than your results might differ (be >wrong) a bit or a lot.I usually say that few things, if any, work in absolutes. Most things work in some sort of a spectrum where there are two opposite extreme opinions and all kind of opinions in between. You two agree more than not in my opinion. It seems to me that an "ill-defined" Hamiltonian is something similar to, say, a Hamiltonian that is "different from the 'correct' Hamiltonian." I think you two agree more that you imagined, and disagree only in less relevant details. I think the next link will give you some insights into the agrement/disagrement above:https://medium.com/starts-with-a-bang/don-t-trust-your-theoretical-proof-62ab804ea3d6https://medium.com/starts-with-a-bang/numbers-game-a5546123a213I am sorry if some of you think this article do not belong to this lists, but I believe they can help us guide development of new methods, and gromacs design. Also, the articles help bridge the disagreement about the Hamiltonian.  Noel Carrascal 		 	   		  
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