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PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules. (English) Zbl 1089.92010

Summary: 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.

MSC:

92C40 Biochemistry, molecular biology
92-04 Software, source code, etc. for problems pertaining to biology
81V55 Molecular physics

Keywords:

program package

Software:

PEACH; ABINIT-MP
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