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PLAMAS: Program package for Protein, Liquid, Amorphous, and Molecular Assembly (QM/MM molecular dynamics simulation program for large molecules)
Energy calculations, Structure Optimizations (Steepest Decent, Conjugate Gradient, BFGS, L-BFGS, Fire, Quick min algorithm), Molecular dynamics simulations (Constant energy, Periodic boundary conditions, Ewald method, Constant temperature: Nese-Hoover thermostat, Belly algorithm, Response Kernel Approximation), Electron (Hole) transfer integral: Marcus theory, Electron (Hole) mobility calculations, Free energy gradient, Nudged elastic band, Free energy reaction path optimization, Free energy contribution analysis
Reference of original techniques used in this program.
Charge and atom dipole response kernel approximation for QM(CDRK)/MM method. Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in QM/MM scheme , Asada,K.Ando,K.Sakurai,S.Koseki,M.Nagaoka, Phys.Chem.Chem.Phys.,17, 26955 – 26968 (2015).
Free Energy Contribution Analysis using Response Kernel Approximation: Insights into the Acylation Reaction for beta–lactamase, T.Asada, K.Ando, P.Bandyopadhyay, S.Koseki, J.Phys.Chem.B, 120, 9338-9346 (2016).
Hole transfer integral calculations and hole mobility in the amorphous phase. Amorphous Solid Simulation and Trial Fabrication of the Organic Field-Effect Transistor of Tetrathienonaphthalenes Prepared by Using Microflow Photochemical Reactions; A Theoretical Calculation-Inspired Investigation, Yamamoto, Atsushi; Matsui, Yasunori; Asada, Toshio; Kumeda, Motoki; Takagi, Kenichiro; Suenaga, Yu; Nagae, Kunihiko; Ohta, Eisuke; Sato, Hiroyasu; Koseki, Shiro; Naito, Hiroyoshi; Ikeda, Hiroshi, J.Org.Chem.,81, 3168-3176 (2016).