Finite temperature string method

W. E, W. Ren, and E. Vanden-Eijnden (2005) Finite Temperature String Method for the Study of Rare Events. J. Phys. Chem. B, 109, pp. 6688-6693 R. Fiber, A. Ghosh, A. Cardenas, and H. Stern (2004) Bridging the gap between reaction pathways, long time dynamics and calculation of rates. Adv. Chem. Phys., 126, pp. 93-129... 

To generalize the zero- or the finite-temperature string methods to work in collective variables (Sects. 6.4 and 6.5), it suffices to do the following. At each iteration, it is now required to estimate the tensor A fiO) defined in (94) and determine the gradient of the density M 9) defined in (93) to be used in the equivalent of (125) (in the zero-temperature version) or sample with respect to this density to identify the equivalent of (127) (in the finite-temperature version). This requires to introduce an additional loop of sampling of blue moon type, now in the original ensemble with density m(x) under the additional constraint that 0 x) = 6. For details, see [23]. 

W. E, W. Ren and E. Vanden-Eijnden (2005) Finite temperature string method for the study of rare events. J. Phys. Chem. B 109, p. 6688... 

W. Ren, E. Vanden-Eijnden, P. Maragakis, and W. E. (2005) Transition pathways in complex systems Application of the finite-temperature string method to the alanine dipeptide. J. Chem. Phys. 123, 134109... 

The elastic band method has been applied with remarkable success.63,64 However, it cannot be applied to problems that have rugged energy landscapes, like proteins. Recently, a similar method has been developed, that was designed to be applicable to rugged landscape systems. It is called the finite-temperature string method .65... 

Vanden-Eijnden, E., VentmoU, M. Revisiting the finite temperature string method for the calculation of reaction mbes and free energies. J. Chem. Phys. 130, 194103 (2009)... 

Transition Pathways in Complex Systems Application of the Finite-Temperature String Method to the Alanine Dipeptide. 

E. Vanden-Eijnden and M. Venturoh,/. Chem. Phys., 130(19), 194103 (2009). Revisiting the Finite Temperature String Method for the Calculation of Reaction Tubes and Free Energies. 

The string method is particularly suitable for studying systems evolving stochastically in the overdamped limit. The reason is that in the finite temperature string method one makes the assumption that once the system has entered B coming from A, any ttansition from B back to A is statistically uncorrelated. To satisfy this requirement the stable states A and B need to be appropriately defined, possibly in... 

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