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Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry
Author(s) -
Gibson Kenneth D.,
Scheraga Harold A.
Publication year - 1990
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540110406
Subject(s) - series (stratigraphy) , fixed point , equations of motion , mathematics , molecular dynamics , space (punctuation) , differential equation , variable (mathematics) , mathematical analysis , classical mechanics , physics , computer science , computational chemistry , chemistry , paleontology , biology , operating system
A new algorithm is presented for performing molecular dynamics simulations of peptides with fixed geometry, with the aim of simulating conformational changes and of exploring conformational space. The principle of the method is to expand the potential energy as a Taylor's series in the coordinates around the current point, retaining the force and its first two derivatives, and obtain a series solution of the resulting differential equations using a method due to Lyapunov. By choosing the time step so that the second term in the series is small compared to the first, the true solution can in principle be approximated to any desired degree of accuracy. The algorithm has been used to solve numerically Lagrange's equations of motion for N ‐acetyl alanine amide and N ‐acetyl methionide amide, regarded as fixed at their C ‐termini, under the influence of the ECEPP/2 potential energy function, and time steps of 15–30 fsec have been achieved with little variation in the total energy. Possible directions for future development are discussed.