Journal of Computational Chemistry

Cover image for Vol. 39 Issue 3

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.229

ISI Journal Citation Reports © Ranking: 2016: 55/166 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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Recently Published Articles

  1. Single-pass incremental force updates for adaptively restrained molecular dynamics

    Krishna Kant Singh and Stephane Redon

    Version of Record online: 11 DEC 2017 | DOI: 10.1002/jcc.25126

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    The figure represents the configuration space explore by all-atom molecular dynamics and adaptively restrained molecular dynamics (with different restraining parameters) simulations. Adaptively switching the positional degrees of freedom on and off not only allows to perform more number of integration steps in wall clock time but also produces the unbiased and equilibrium statistics of the system.

  2. Do surfaces of positive electrostatic potential on different halogen derivatives in molecules attract? like attracting like!

    Arpita Varadwaj, Pradeep R. Varadwaj and Koichi Yamashita

    Version of Record online: 11 DEC 2017 | DOI: 10.1002/jcc.25125

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    The graph illustrates that whereas attraction between similarly charged species is against Coulomb's law, this is not impossible when the dispersion contribution to the binding energy is unexpectedly large.

  3. Reverse mapping method for complex polymer systems

    Jakub Krajniak, Zidan Zhang, Sudharsan Pandiyan, Eric Nies and Giovanni Samaey

    Version of Record online: 6 DEC 2017 | DOI: 10.1002/jcc.25129

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    This article provides an extension to the generic adaptive resolution reverse mapping, which allows easily to transform from a coarse-grained representation to atomistic for the dynamically crosslinked complex polymer systems like polymer networks or hyperbranched polymers. In principle, reverse mapping can be done on any kind of molecules that are in the coarse-grained representation and the desired atomistic description is available.

  4. Can MM/GBSA calculations be sped up by system truncation?

    Majda Misini Ignjatović, Paulius Mikulskis, Pär Söderhjelm and Ulf Ryde

    Version of Record online: 26 NOV 2017 | DOI: 10.1002/jcc.25120

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    We have studied whether calculations of the binding free energy of small ligands to a protein by the MM/GBSA approach can be sped up by including only a restricted number of atoms close to the ligand. If the protein is truncated before the molecular dynamics simulations, quite large changes are observed for the calculated binding energies, but the results are strongly improved if no atoms are fixed in the simulations. If energies are calculated on snapshots that are truncated after the simulation, the average error is less than 1 kJ/mol at 8.5 Å truncation radius.

  5. Testing the limits of model membrane simulations—bilayer composition and pressure scaling

    Nikoleta Ivanova and Anela Ivanova

    Version of Record online: 21 NOV 2017 | DOI: 10.1002/jcc.25117

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    Statistical analysis of 1 μs long atomistic MD simulations of two types of model membranes (DPPC and mixture of five lipids) with an isotropic or semi-isotropic pressure scaling in the presence of a cell-penetrating drug-peptide complex (DOX-CPP) shows that the lipid composition of the bilayer and the pressure scaling method are essential for accurate reproduction of the initial penetration stages of the DOX-CPP translocation.