title: Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.
abstract: Precise and rapid calculation of long-range interactions is of crucial importance for molecular dynamics (MD) and Monte Carlo simulations. Instead of the Ewald method or its high speed variant, PME, we applied our novel method, called the force-switching Wolf method, to computation of the free energy landscapes of a short peptide in explicit water. Wolf and co-workers showed that long-range electrostatic energy under a periodic boundary condition can be well reproduced even by truncating the contribution from the distant charges, when the charge neutrality is taken into account. We recently applied the procedure proposed by Wolf and co-workers to a mathematically consistent MD theory by means of a force-switching scheme, and we show that the total electrostatic energy for sodium chloride liquid was well conserved and stable during the MD simulation with the force-switching Wolf method. Our current results for an aqueous peptide solution with a series of canonical and multicanonical molecular dynamics simulations show that the force-switching Wolf method is not only in good accordance with the energies and forces calculated by the conventional PME method but also properly reproduces the solvation and the free energy landscapes of the peptide at 300 K.
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Yasushige
authors.initials: Y
authors.lastname: Yonezawa
authors.affiliation: Computational Science Research Program, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Ikuo
authors.initials: I
authors.lastname: Fukuda
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Narutoshi
authors.initials: N
authors.lastname: Kamiya
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Hiromitsu
authors.initials: H
authors.lastname: Shimoyama
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura