By Jiali Gao, Mark A. Thompson
content material: Quantum mechanical-molecular mechanical coupled potentials / Kenneth M. Merz, Jr. --
Quantum mechanical-molecular mechanical methods for learning chemical reactions in proteins and answer / Jörg Bentzien, Jan Florián, Timothy M. Glennon, and Arieh Warshel --
The geometry of water in liquid water from hybrid ab initio-Monte Carlo and density functional-molecular dynamics simulations / Cristobal Alhambra, Kyoungrim Byun, and Jiali Gao --
at the therapy of hyperlink atoms in hybrid equipment / Iris Antes and Walter Thiel --
a style of hybrid quantum-classical calculations for giant organometallic-metallobiochemical structures : purposes to iron picket-fence porphyrin and nutrition B12 / Isaac B. Bersuker, Max ok. Leong, James E. Boggs, and Robert S. Pearlman --
a technique for quantum molecular modeling of constitution and reactivity at solid-liquid interfaces / Eugene V. Stefanovich and Thanh N. Truong --
Dual-level tools for digital constitution calculations of strength power services that use quantum mechanics because the reduce point / José C. Corchado and Donald G. Truhlar --
A mixed Car-Parrinello quantum mechanical-molecular mechanical implementation for ab initio molecular dynamics simulations of prolonged structures / Tom okay. Woo, Peter M. Margl, Liqun Deng, and Tom Ziegler --
The molecular mechanics valence bond process : digital constitution and semiclassical dynamics : functions to difficulties in photochemistry / Michael J. Bearpark, Barry R. Smith, Fernando Bernardi, Massimo Olivucci, and Michael A. Robb --
Density sensible idea ab initio molecular dynamics and mixed density useful concept and molecular dynamics simulations / Dongqing Wei and Dennis R. Salahub --
Generalized molecular mechanics together with quantum digital constitution edition of polar solvents : an summary / Hyung J. Kim, Badry D. Bursulaya, Jonggu Jeon, and Dominic A. Zichi --
RISM-SCF examine of solvent influence on digital constitution and chemical response in answer : temperature dependence of pKw / Fumio Hirata, Hirofumi Sato, Seiichiro Ten-no, and Shigeki Kato --
common solvation versions / Gregory D. Hawkins, Tianhai Zhu, Jiabo Li, Candee C. Chambers, David J. Giesen, Daniel A. Liotard, Christopher J. Cramer, and Donald G. Truhlar --
Quantum mechanical-molecular mechanical calculations of (hyper- )polarizabilities with the direct response box method / Piet Th. van Duijnen, Marcel Swart, and Ferdinand Grozema --
The neighborhood self-consistent box rules and functions to mixed quantum mechanical-molecular mechanical computations on biomacromolecular platforms / Xavier Assfeld, Nicolas Ferré, and Jean-Louis Rivail --
Investigating enzyme response mechanisms with quantum mechanical-molecular mechanical plus molecular dynamics calculations / Peter L. Cummins and Jill E. Gready --
Ab initio and hybrid molecular dynamics simulations of the lively web site of human carbonic anhydrase II : a attempt case research / Ursula Röthlisberger --
software of linear-scaling digital constitution tips on how to the examine of polarization of proteins and DNA in answer / Darrin M. York --
interesting eco-friendly fluorescent protein / Volkhard Helms, Erik F.Y. Hom, T.P. Straatsma, J. Andrew McCammon, and Peter Langhoff.
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In computing intermolecular interactions, periodic boundary conditions are used, along with a spherical cutoff distance of 9 Â. The Monte Carlo simulations included at 2 10 configurations of equilibration followed by 4 10 configurations of averaging for each calculation. Subsequently, stochastic boundary molecular dynamics (SBMD) simulations (36) were carried out in a 20 sphere of 1024 TIP3P water molecules using the DFT/T1P3P potential. The Q M water molecule is approximately located near the center of the sphere, and its geometry is fully relaxed throughout the simulation.