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 [Chem.Phys. Lett. 313 (1999) 701], into PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities of the package were demonstrated. First, high parallel efficiency of FMO was demonstrated in a single point calculation of a protein. Second,FMO-MD simulations [Chem. Phys. Lett. 372 (2003) 342] 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.
Komeiji
Yuto
Y
National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 2, Japan. komeiji@aist.go.jp
Inadomi
Yuichi
Y
Nakano
Tatsuya
T
D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004744:Enkephalin, Methionine / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D009841:Oligonucleotides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D013997:Time Factors; D014867:Water / Q000737:chemistry
D009841:Oligonucleotides; D011506:Proteins; D014867:Water; D004744:Enkephalin, Methionine