Geodesic
Net-Q Model with Charge Transfer and Polarization for Molecular Dynamics
Sibirskij žurnal čistoj i prikladnoj matematiki, Tome 13 (2013) no. 4, pp. 153-170 Cet article a éte moissonné depuis la source Math-Net.Ru

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The article describes a new method for dynamic correction of the atom charges for molecular dynamics. The proposed method can be regarded as an extension of the QEq, QTPIE and fluq-q methods. The method is based on a graph which represents the molecular system and allows for charges to be transferred along its edges only. An advantage of the method is that its computational complexity is linear, in contrast to a polynomial one of the QEq and QTPIE. The proposed method correctly describes the charge distribution in the dissociation limit. A comparison of docked ligand positions in a number of the protein-ligand complexes with adjusted charges by the net-q model shows that they are less different from the crystallographic positions than those obtained by using fixed charges.
Mots-clés : charge equilibration
Keywords: charge transfer, polarization, molecular dynamics. 
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     author = {E. S. Fomin and A. E. Vasenin},
     title = {Net-Q {Model} with {Charge} {Transfer} and {Polarization} for {Molecular} {Dynamics}},
     journal = {Sibirskij \v{z}urnal \v{c}istoj i prikladnoj matematiki},
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E. S. Fomin; A. E. Vasenin. Net-Q Model with Charge Transfer and Polarization for Molecular Dynamics. Sibirskij žurnal čistoj i prikladnoj matematiki, Tome 13 (2013) no. 4, pp. 153-170. http://geodesic.mathdoc.fr/item/VNGU_2013_13_4_a11/

[1] Phillips J. C., Stone J. E., “Probing Biomolecular Machines with Graphics Processors”, Communications of the ACM, 52:10 (2009), 34–41 | DOI

[2] Fomin E. S., “Consideration of Data Load Time on Modern Processors for the Verlet Table and Linked Cell Algorithms”, J. Comp. Chem., 32:7 (2011), 1386–1399 | DOI

[3] Chirlian L. E., Francl M. M., “Atomic Charges Derived from Electrostatic Potentials: A Detailed Study”, J. Comp. Chem., 8 (1987), 894–903 | DOI

[4] Cho A. E., Guallar V., Berne B. J., Friesner R., “Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach”, J. Comp. Chem., 26 (2005), 915–931 | DOI

[5] Sanderson R. T., “An Interpretation of Bond Lengths and Classification of Bonds”, Science, 114 (1951), 670–672 | DOI

[6] Mortier W. J., Ghosh S. K., Shankar S. J., “Electronegativity-Equalization Method for the Calculation of Atomic Charges in Molecules”, Am. Chem. Soc., 108 (1986), 4315–4320 | DOI

[7] Rick S. W., Stuart S. J., Berne B. J., “Dynamical Fluctuating Charge Force Fields: Application to Liquid Water”, J. Chem. Phys., 101 (1994), 6141–6156 | DOI

[8] York D. M., Yang W., “A Chemical Potential Equalization Method for Molecular Simulations”, J. Chem. Phys., 104 (1996), 159–172 | DOI

[9] Rappe A. K., Goddard W. A., “Charge Equilibration for Molecular Dynamics Simulations”, J. Phys. Chem., 95 (1991), 3358–3363 | DOI

[10] Zhu S. B., Singh S., Robinson G. W., “A New Flexible/Polarizable Water Model”, J. Chem. Phys., 95 (1991), 2791 | DOI

[11] Chen B., Potoff J. J., Siepmann J. I., “Adiabatic Nuclear and Electronic Sampling Monte Carlo Simulations in the Gibbs Ensemble: Application to Polarizable Force Fields for Water”, J. Phys. Chem. B, 104 (2000), 2378–2390 | DOI

[12] Doklady Chemistry, 375:4–6 (2000), 281–284 | DOI | Zbl

[13] Bayly C. I., Cieplak P., Cornell W. D., Kollman P. A., “Electrostatic Potential Based Method Using Charge Restraints For Determining Atom-Centered Charges: The RESP Model”, J. Phys. Chem., 97 (1993), 10269 | DOI

[14] Doklady Chemistry, 408:1 (2006), 76–79 | DOI

[15] Rosen N., “Calculation of Interaction between Atoms with S-Electrons”, Phys. Rev., 38 (1931), 255–276 | DOI

[16] Andersen H. C., “Molecular Dynamics at Constant Pressure and/or Temperature”, J. Chem. Phys., 72 (1980), 2384–2393 | DOI

[17] Rick S. W., Stuart S. J., Berne B. J., “Potentials and Algorithms for Incorporating Polarizability in Computer Simulation”, Review in Computational Chemistry, 18 (2002), 89–146

[18] Morales J., Martinez T. J., “Classical Fluctuating Charge Theories: The Maximum Entropy Valence Bond Method and Relationships to Previous Models”, J. Phys. Chem., 105A (2001), 2842 | DOI

[19] Chen J., Martinez T. J., “QTPIE: Charge Transfer with Polarization Current Equalization. A Fluctuation Charge Model with Correct Asymptotics”, Chem. Phys. Letters, 438 (2007), 315–320 | DOI

[20] Chen J., Hundertmark D., Martinez T. J., “A Unified Theoretical Framework for Fluctuating-Charge Models in Atom-Space and in Bond-Space”, J. Chem. Phys., 129 (2008), 214113 | DOI

[21] Course of Theoretical Physics, v. 1, Mechanics, Third Edition, Butterworth-Heinemann, 1976

[22] Biophysics, 51:1, Supplement (2006), 110–112 | DOI | MR

[23] Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E., “The Protein Data Bank”, Nucl. Acids Res., 28:1 (2000), 235–242 | DOI