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Mass-zero constrained molecular dynamics for electrostatic interactions
Federica Troni, Davide Grassano, Jayashree Narayan, Benoît Roux and Sara Bonella The Journal of Chemical Physics 163(21) (2025) https://doi.org/10.1063/5.0283356
Molecular simulation and experimental validation for surface tension of new Low-GWP refrigerant mixtures R32/CF3I and R1123/CF3I
Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins
Olivier Bignucolo, Christophe Chipot, Stephan Kellenberger and Benoît Roux The Journal of Physical Chemistry B 126(36) 6868 (2022) https://doi.org/10.1021/acs.jpcb.2c04593
Interaction of Phthalates with Lipid Bilayer Membranes
Zobia Naz, Roshan Shrestha, Syed Tarique Moin and Luca Monticelli The Journal of Physical Chemistry B 126(25) 4679 (2022) https://doi.org/10.1021/acs.jpcb.2c02007
A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V
Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field
Yan M. H. Gonçalves, Caroline Senac, Patrick F. J. Fuchs, Philippe H. Hünenberger and Bruno A. C. Horta Journal of Chemical Theory and Computation 15(3) 1806 (2019) https://doi.org/10.1021/acs.jctc.8b00425
String Method for Protein–Protein Binding Free-Energy Calculations
Donghyuk Suh, Sunhwan Jo, Wei Jiang, Chris Chipot and Benoît Roux Journal of Chemical Theory and Computation 15(11) 5829 (2019) https://doi.org/10.1021/acs.jctc.9b00499
Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids
Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation
Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization
Classical Electrostatics for Biomolecular Simulations
G. Andrés Cisneros, Mikko Karttunen, Pengyu Ren and Celeste Sagui Chemical Reviews 114(1) 779 (2014) https://doi.org/10.1021/cr300461d
Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods
Ming Huang, Timothy J. Giese, Tai-Sung Lee and Darrin M. York Journal of Chemical Theory and Computation 10(4) 1538 (2014) https://doi.org/10.1021/ct401013s
Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation
Rolf E. Isele-Holder, Wayne Mitchell, Jeff R. Hammond, Axel Kohlmeyer and Ahmed E. Ismail Journal of Chemical Theory and Computation 9(12) 5412 (2013) https://doi.org/10.1021/ct4004614
How to Convert SPME to P3M: Influence Functions and Error Estimates
V. Ballenegger, J. J. Cerdà and C. Holm Journal of Chemical Theory and Computation 8(3) 936 (2012) https://doi.org/10.1021/ct2001792
Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
Maria M. Reif, Vincent Kräutler, Mika A. Kastenholz, Xavier Daura and Philippe H. Hünenberger The Journal of Physical Chemistry B 113(10) 3112 (2009) https://doi.org/10.1021/jp807421a
Biophysical Techniques in Photosynthesis
William W. Parson and Arieh Warshel Advances in Photosynthesis and Respiration, Biophysical Techniques in Photosynthesis 26 401 (2008) https://doi.org/10.1007/978-1-4020-8250-4_20
The optimal P3M algorithm for computing electrostatic energies in periodic systems
Long range interactions on wires: A reciprocal space based formalism
Peter Mináry, Joseph A. Morrone, Dawn A. Yarne, Mark E. Tuckerman and Glenn J. Martyna The Journal of Chemical Physics 121(23) 11949 (2004) https://doi.org/10.1063/1.1806403
Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
Celeste Sagui, Lee G. Pedersen and Thomas A. Darden The Journal of Chemical Physics 120(1) 73 (2004) https://doi.org/10.1063/1.1630791
A new reciprocal space based treatment of long range interactions on surfaces
Peter Mináry, Mark E. Tuckerman, Katianna A. Pihakari and Glenn J. Martyna The Journal of Chemical Physics 116(13) 5351 (2002) https://doi.org/10.1063/1.1453397
Computational Methods for Macromolecules: Challenges and Applications
Mark E. Tuckerman, Peter Minary, Katianna Pihakari and Glenn J. Martyna Lecture Notes in Computational Science and Engineering, Computational Methods for Macromolecules: Challenges and Applications 24 381 (2002) https://doi.org/10.1007/978-3-642-56080-4_16
FROM FOLDING THEORIES TO FOLDING PROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding
Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions