PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules. A program package for molecular simulations of biological molecules was developed. The package, “PEACH version 4 with ABINIT-MP version 20021029”, was constructed by incorporating ABINIT-MP, a program for the fragment molecular orbital (FMO) method [K. Kitaura et al., Chem. Phys. Lett. 313, 701–706 (1999)], into PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities of the package were demonstrated. First, the high parallel efficiency of FMO was demonstrated in a single point calculation of a protein. Second, FMO-MD simulations [Y. Komeiji, ibid. 342–347 (2003)] of a peptide were performed with and without explicit solvent, and the simulations showed the influence of the solvent on the electronic state of the peptide.
Keywords for this software
References in zbMATH (referenced in 4 articles , 1 standard article )
Showing results 1 to 4 of 4.
- Korchowiec, Jacek; Gu, Feng Long; Aoki, Yuriko: Elongation method for linear scaling SCF calculations of polymers (2006)
- Nemoto, Tadashi; Fedorov, Dmitri G.; Uebayasi, Masami; Kanazawa, Kenji; Kitaura, Kazuo; Komeiji, Yuto: Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein (2005)
- Komeiji, Yuto; Inadomi, Yuichi; Nakano, Tatsuya: PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules (2004)
- Zhang, Junwei; Aizawa, Masahiro; Amari, Shinji; Iwasawa, Yoshio; Nakano, Tatsuya; Nakata, Kotoko: Development of $Ki$Bank, a database supporting structure-based drug design (2004)