String method for freely tumbling system

Data pubblicazione: Sep 27, 2013 12:35:31 AM

String method is a technique to calculate minimum free energy paths for reaction mechanism that go from a reactant to a product. The "string" is a set of states that smoothly goes from one state to the other via certain descriptors. 

In the past it was possible to do this by using only internal coordinates like distances, torsion and so forth. Of course the best choice would be using cartesian coordinates that may produce a complete set of forces in every direction but this was requiring to fix the system in space. This is really weird, especially when your reaction is happening while tumbling and can produce artifacts or irrealistic results. There are many examples of interesting problems that might suffer from it: inward/outward conformational transition of membrane-embedded transporter is a nice case. Similarly for drug binding. So I came with the idea, that some might not like, to use an optimal alignment algorithm to  remove rototranslations, while leaving the system free. This nicely converges and is extremely simple to set up, which I like a lot. You can find the article on JCTC. Additionally you can understand much more from your reaction since you can "decompose" the contribution of free energy on a "per atom" basis and see who is the guilty part for your reaction. That's cool! And you have nice arrows that tell you where the atoms pull you along the reaction! Jose` Faraldo-Gomez helped me a lot with this and we got also very helpful interactions with Luca Maragliano and Eric Vanden-Eijnden.