Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems

A new computational technique is presented to calculate approximate reaction paths in complex molecules. The method is based on the Gaussian chain approach proposed by Elber and Karplus [1] but avoids some computational difficulties of this technique. It is also more than 10 times faster. The new formulation is quite general and enables empirical interpolation between two types of motions which differ considerably: trapped and ballistic (see also “Note Added in Proof”). We present test results for two model molecules: alanine dipeptide (AD) and isobutyryl-(ala)3-NH-methyl (IAN). The optimization of the chain is very stable and provides an approximate continuous path even if the initial guess is poor.