Journal of Computational Chemistry

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Vectorization of the general Monte Carlo classical trajectory program VENUS
Journal of Computational Chemistry - Tập 12 Số 8 - Trang 1014-1024 - 1991
Xiche Hu, William L. Hase, Tony Pirraglia
AbstractThe general chemical dynamics computer program VENUS is used to perform classical trajectory simulations for large polyatomic systems, with many atoms and complicated potential energy functions. To simulate an ensemble of many trajectories requires a large amount of CPU time. Since each trajectory is independent, it is possible to parallel process a large s...... hiện toàn bộ
13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models
Journal of Computational Chemistry - Tập 30 Số 2 - Trang 222-235 - 2009
Anmin Zheng, Shang-Bin Liu, Feng Deng
AbstractPrecise theoretical predictions of NMR parameters are helpful for the spectroscopic identification of complicated biological molecules, especially for the carbon shielding tensors in amino acids. The 13C shielding tensors of various crystalline amino acids and peptides have been calculated using the gauge‐including projector augmented w...... hiện toàn bộ
Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations
Journal of Computational Chemistry - Tập 30 Số 12 - Trang 1799-1815 - 2009
Séverine Queyroy, Haruki Nakamura, Ikuo Fukuda
AbstractThis article illustrates practical applications to molecular dynamics simulations of the recently developed numerical integrators [Phys Rev E 2006, 73, 026703] for ordinary differential equations. This method consists of extending any set of ordinary differential equations in order to define a time invariant function, and then use the techniques of divergen...... hiện toàn bộ
Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics
Journal of Computational Chemistry - Tập 11 Số 4 - Trang 440-467 - 1990
Fariborz Mohamadi, Nigel G. J. Richards, Wayne C. Guida, Rob M. J. Liskamp, Mark A. Lipton, Craig E. Caufield, George Chang, Thomas F. Hendrickson, W. Clark Still
AbstractAn integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom‐based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state‐of‐...... hiện toàn bộ
Ability of the PM3 quantum‐mechanical method to model intermolecular hydrogen bonding between neutral molecules
Journal of Computational Chemistry - Tập 14 Số 1 - Trang 89-104 - 1993
Marcus W. Jurema, George C. Shields
AbstractThe PM3 semiempirical quantum‐mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02–0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an ...... hiện toàn bộ
The Computer System G R A P H: A Useful Tool in Chemical Graph Theory
Journal of Computational Chemistry - Tập 7 Số 5 - Trang 640-644 - 1986
Dragoš Cvetković, Iván Gutman
AbstractThe interactive programming system GRAPH, implemented at the Faculty of Electrical Engineering in Belgrade, is described. This system has been designed to treat a great variety of problems of graph theory. In the present article we point out the applicability of the system GRAPH in chemical investigations and illustrate it by two examples.
Coarse‐graining: A procedure to generate equilibrated and relaxed models of amorphous polymers
Journal of Computational Chemistry - Tập 28 Số 12 - Trang 1929-1935 - 2007
David Curcó, Carlos Alemán
AbstractWe present a coarse‐graining procedure to construct models of amorphous polymers. The method, which was applied to polyethylene, is based on a generation–relaxation strategy previously developed to provide independent atomistic microstructures. The coarse‐graining was performed by assigning positions to mesoscopic particles denoted blobs, which represent gr...... hiện toàn bộ
KiSThelP: A program to predict thermodynamic properties and rate constants from quantum chemistry results†
Journal of Computational Chemistry - Tập 35 Số 1 - Trang 82-93 - 2014
Sébastien Canneaux, Frédéric Bohr, Éric Hénon
Kinetic and Statistical Thermodynamical Package (KiSThelP) is a cross‐platform free open‐source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, and NWChem). Some key features are: gas‐phase molecular thermodynamic properties (offering hindered rotor treat...... hiện toàn bộ
Implementing dimer metadynamics using gromacs
Journal of Computational Chemistry - Tập 39 Số 25 - Trang 2126-2132 - 2018
M. Nava
We develop a Gromacs implementation of dimer metadynamics (DM) (JCTC 13, 425 [2017]) for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this purpose, the fine tuning of Gromacs input parameters, modified forcefields and custom nonbonded interactions. We demonstrate this implementation on alani...... hiện toàn bộ
Accurate description of van der Waals complexes by density functional theory including empirical corrections
Journal of Computational Chemistry - Tập 25 Số 12 - Trang 1463-1473 - 2004
Stefan Grimme
AbstractAn empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT‐D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R...... hiện toàn bộ
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