Atomic stress tensor analysis of proteins

We performed stress tensor analysis of polypeptides at the atomic level by molecular dynamics simulations. Most of the approaches to stress tensor analysis of molecules in the literature assume that the interatomic forces are pairwise; however commonly used force-field functions contain multi-body interactions. To address this issue, we derived new mathematical formulae for atomic forces based on force-field functions, in which the total force acting on each atom is expressed as a summation of pairwise interatomic forces. Then, a computer program for stress tensor analysis was developed, and it successfully characterized the mechanical features of molecules at the atomic level.