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    JCC
    2006
    110views more  JCC 2006»
    Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm
    13 years 4 months ago
    Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm
    Download  www.remo-rohs.de
    : This article describes a method for solving the geometric closure problem for simplified models of nucleic acid structures by using the constant bond lengths approximation. The r...
    Heinz Sklenar, Daniel Wüstner, Remo Rohs
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    JCC
    2006
    51views more  JCC 2006»
    Study of peptide conformation in terms of the ABEEM/MM method
    13 years 4 months ago
    Study of peptide conformation in terms of the ABEEM/MM method
    Download  www.scichina.com
    Zhong-Zhi Yang, Qiang Zhang
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    JCC
    2006
    86views more  JCC 2006»
    An algorithm for three-dimensional Voronoi S-network
    13 years 4 months ago
    An algorithm for three-dimensional Voronoi S-network
    Download  www.physics.usyd.edu.au
    : The paper presents an algorithm for calculating the three-dimensional Voronoi
    Nikolai N. Medvedev, V. P. Voloshin, V. A. Luchnik...
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    JCC
    2006
    103views more  JCC 2006»
    Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
    13 years 4 months ago
    Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
    Download  www.mpibpc.mpg.de
    : The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
    Oliver F. Lange, Lars V. Schäfer, Helmut Grub...
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    JCC
    2006
    39views more  JCC 2006»
    A theoretical study of thermal [1, 3]-sigmatropic rearrangements of 3-trimethylsilyl-1-pyrazoline: Concerted vs. stepwise mechan
    13 years 4 months ago
    A theoretical study of thermal [1, 3]-sigmatropic rearrangements of 3-trimethylsilyl-1-pyrazoline: Concerted vs. stepwise mechan
    Download  qchem.knu.ac.kr
    Abstract: Possible reaction mechanisms of 1,3-silyl and 1,3-hydrogen thermal rearrangements of trimethylsilyl-1pyrazoline and its model systems were theoretically explored using B3...
    Chultack Lim, Hee Soon Lee, Young-Woo Kwak, Cheol ...
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    JCC
    2006
    82views more  JCC 2006»
    Monte Carlo simulations of biomolecules: The MC module in CHARMM
    13 years 4 months ago
    Monte Carlo simulations of biomolecules: The MC module in CHARMM
    Download  dinner-group.uchicago.edu
    : We describe the implementation of a general and flexible Monte Carlo (MC) module for the program CHARMM, which is used widely for modeling biomolecular systems with empirical ene...
    Jie Hu, Ao Ma, Aaron R. Dinner
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    JCC
    2006
    68views more  JCC 2006»
    Explicit factorization of external coordinates in constrained statistical mechanics models
    13 years 4 months ago
    Explicit factorization of external coordinates in constrained statistical mechanics models
    Download  neptuno.unizar.es
    If a macromolecule is described by curvilinear coordinates or rigid constraints are imposed, the equilibrium probability density that must be sampled in Monte Carlo simulations in...
    Pablo Echenique, Iván Calvo
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    JCC
    2006
    60views more  JCC 2006»
    A charge-scaling implementation of the variational electrostatic projection method
    13 years 4 months ago
    A charge-scaling implementation of the variational electrostatic projection method
    Download  static.msi.umn.edu
    Brent A. Gregersen, Darrin M. York
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    JCC
    2006
    61views more  JCC 2006»
    Ab initio QM/MM dynamics of H3O+ in water
    13 years 4 months ago
    Ab initio QM/MM dynamics of H3O+ in water
    Download  chem.hamilton.edu
    : A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure ...
    Pathumwadee Intharathep, Anan Tongraar, Kritsana S...
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    JCC
    2006
    42views more  JCC 2006»
    Starting SCF calculations by superposition of atomic densities
    13 years 4 months ago
    Starting SCF calculations by superposition of atomic densities
    Download  www.public.iastate.edu
    : We describe the procedure to start an SCF calculation of the general type from a sum of atomic electron densities, as implemented in GAMESS-UK. Although the procedure is well kno...
    J. H. Van Lenthe, R. Zwaans, Huub J. J. Van Dam, M...
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