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JCC
2011
105views more  JCC 2011»
12 years 11 months ago
Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
Abstract: Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have b...
Michele Seeber, Angelo Felline, Francesco Raimondi...
JCC
2007
79views more  JCC 2007»
13 years 4 months ago
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
Abstract: A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with HartreeFock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capab...
H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. ...
JCC
2007
121views more  JCC 2007»
13 years 4 months ago
Speeding up parallel GROMACS on high-latency networks
: We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clust...
Carsten Kutzner, David van der Spoel, Martin Fechn...
JCC
2007
82views more  JCC 2007»
13 years 4 months ago
Peptide reagent design based on physical and chemical properties of amino acid residues
: It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical...
Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Cheng-Hua Wang,...
JCC
2007
162views more  JCC 2007»
13 years 4 months ago
Bond electron pair: Its relevance and analysis from the quantum chemistry point of view
: This paper first comments on the surprisingly poor status that Quantum Chemistry has offered to the fantastic intuition of Lewis concerning the distribution of the electrons in ...
Jean-Paul Malrieu, Nathalie Guihéry, Carmen...