docs/references.bib
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@article{Mobley2006:orientational-restraints,
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@misc{Ponder,
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@article{Shirts2013:yank,
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@article{Chodera2011,
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}
@incollection{Shoemake1992,
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editor = {Kirk, D.},
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}
@article{Chodera2016,
author = {Chodera, John D.},
title = {A Simple Method for Automated Equilibration Detection in Molecular Simulations},
journal = {Journal of Chemical Theory and Computation},
volume = {12},
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doi = {10.1021/acs.jctc.5b00784},
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URL = {http://dx.doi.org/10.1021/acs.jctc.5b00784},
eprint = {http://dx.doi.org/10.1021/acs.jctc.5b00784}
}
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%@article{Andersen1980,
author = {Andersen, Hans C.},
title = {Molecular dynamics simulations at constant pressure and/or temperature},
journal = {Journal of Chemical Physics},
volume = {72},
number = {4},
pages = {2384-2393},
year = {1980},
type = {Journal Article}
}
%@article{Aqvist2004,
author = {Åqvist, Johan and Wennerström, Petra and Nervall, Martin and Bjelic, Sinisa and Brandsdal, Bjørn O.},
title = {Molecular dynamics simulations of water and biomolecules with a {Monte Carlo} constant pressure algorithm},
journal = {Chemical Physics Letters},
volume = {384},
pages = {288-294},
year = {2004},
type = {Journal Article}
}
%@article{Ceriotti2010,
author = {Ceriotti, M. and Parrinello, M. and Markland, Thomas E. and Manolopoulos, David E.},
title = {Efficient stochastic thermostatting of path integral molecular dynamics},
journal = {Journal of Chemical Physics},
volume = {133},
number = {12},
year = {2010},
type = {Journal Article}
}
%@article{Chow1995,
author = {Chow, Kim-Hung and Ferguson, David M.},
title = {Isothermal-isobaric molecular dynamics simulations with {Monte Carlo} volume sampling},
journal = {Computer Physics Communications},
volume = {91},
pages = {283-289},
year = {1995},
type = {Journal Article}
}
%@article{Craig2004,
author = {Craig, I. R. and Manolopoulos, David E.},
title = {Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics},
journal = {Journal of Chemical Physics},
volume = {121},
pages = {3368-3373},
year = {2004},
type = {Journal Article}
}
%@article{Duan2003,
author = {Duan, Y.; Wu, C. and Chowdhury, S. and Lee, M.C. and Xiong, G. and Zhang, W. and Yang, R. and Cieplak, P. and Luo, R. and Lee, T.},
title = {A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations},
journal = {Journal of Computational Chemistry},
volume = {24},
pages = {1999-2012},
year = {2003},
type = {Journal Article}
}
%@article{Hall1984,
author = {Hall, Randall W. and Berne, B. J.},
title = {Nonergodicity in path integral molecular dynamics},
journal = {Journal of Chemical Physics},
volume = {81},
number = {8},
year = {1984},
type = {Journal Article}
}
%@article{Hornak2006,
author = {Hornak, V. and Abel, R. and Okur, A. and Strockbine, B. and Roitberg, A. and Simmerling, C.},
title = {Comparison of multiple {Amber} force fields and development of improved protein backbone parameters},
journal = {Proteins},
volume = {65},
pages = {712-725},
year = {2006},
type = {Journal Article}
}
%@article{Izaguirre2010,
author = {Izaguirre, Jesús A. and Sweet, Chris R. and Pande, Vijay S.},
title = {Multiscale dynamics of macromolecules using {Normal Mode Langevin}},
journal = {Pacific Symposium on Biocomputing},
volume = {15},
pages = {240-251},
year = {2010},
type = {Journal Article}
}
%@inbook{Kollman1997,
author = {Kollman, P.A. and Dixon, R. and Cornell, W. and Fox, T. and Chipot, C. and Pohorille, A.},
title = {Computer Simulation of Biomolecular Systems},
editor = {Wilkinson, A. and Weiner, P. and van Gunsteren, Wilfred F.},
publisher = {Elsevier},
volume = {3},
pages = {83-96},
year = {1997},
type = {Book Section}
}
%@article{Labute2008,
author = {Labute, Paul},
title = {The generalized {Born}/volume integral implicit solvent model: Estimation of the free energy of hydration using {London} dispersion instead of atomic surface area},
journal = {Journal of Computational Chemistry},
volume = {29},
number = {10},
pages = {1693-1698},
year = {2008},
type = {Journal Article}
}
%@article{Lamoureux2003,
author = {Lamoureux, Guillaume and Roux, Benoit},
title = {Modeling induced polarization with classical {Drude} oscillators: Theory and molecular dynamics simulation algorithm},
journal = {Journal of Chemical Physics},
volume = {119},
number = {6},
pages = {3025-3039},
year = {2003},
type = {Journal Article}
}
%@article{Li2010,
author = {Li, D.W. and Br{\"u}schweiler, R.},
title = {{NMR}-based protein potentials},
journal = {Angewandte Chemie International Edition},
volume = {49},
pages = {6778-6780},
year = {2010},
type = {Journal Article}
}
%@article{Lindorff-Larsen2010,
author = {Lindorff-Larsen, K. and Piana, S. and Palmo, K. and Maragakis, P. and Klepeis, J. and Dror, R.O. and Shaw, D.E.},
title = {Improved side-chain torsion potentials for the {Amber ff99SB} protein force field},
journal = {Proteins},
volume = {78},
pages = {1950-1958},
year = {2010},
type = {Journal Article}
}
%@article{Liu1989,
author = {Liu, Dong C. and Nocedal, Jorge},
title = {On the Limited Memory {BFGS} Method For Large Scale Optimization},
journal = {Mathematical Programming},
volume = {45},
pages = {503-528},
year = {1989},
type = {Journal Article}
}
%@article{Lopes2013,
author = {Lopes, Pedro E. M. and Huang, Jing and Shim, Jihyun and Luo, Yun and Li, Hui and Roux, Benoît and MacKerell, Alexander D.},
title = {Polarizable Force Field for Peptides and Proteins Based on the Classical {Drude} Oscillator},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {12},
pages = {5430-5449},
year = {2013},
type = {Journal Article}
}
%@article{Markland2008,
author = {Markland, Thomas E. and Manolopoulos, David E.},
title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations},
journal = {Journal of Chemical Physics},
volume = {129},
number = {2},
year = {2008},
type = {Journal Article}
}
%@article{Parrinello1984,
author = {Parrinello, M. and Rahman, A.},
title = {Study of an {F} center in molten {KCl}},
journal = {Journal of Chemical Physics},
volume = {80},
number = {2},
pages = {860-867},
year = {1984},
type = {Journal Article}
}
%@article{Ren2002,
author = {Ren, P. and Ponder, Jay W.},
title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations},
journal = {Journal of Computational Chemistry},
volume = {23},
pages = {1497-1506},
year = {2002},
type = {Journal Article}
}
%@article{Ren2003,
author = {Ren, P. and Ponder, Jay W.},
title = {Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation},
journal = {Journal of Physical Chemistry B},
volume = {107},
pages = {5933-5947},
year = {2003},
type = {Journal Article}
}
%@article{Schnieders2007,
author = {Schnieders, Michael J. and Ponder, Jay W.},
title = {Polarizable Atomic Multipole Solutes in a Generalized {Kirkwood} Continuum},
journal = {Journal of Chemical Theory and Computation},
volume = {3},
pages = {2083-2097},
year = {2007},
type = {Journal Article}
}
%@article{Shi2013,
author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
title = {Polarizable Atomic Multipole-Based {AMOEBA} Force Field for Proteins},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {9},
pages = {4046-4063},
year = {2013},
type = {Journal Article}
}
%@article{Shirts2005,
author = {Shirts, Michael R. and Pande, Vijay S.},
title = {Solvation free energies of amino acid side chain analogs for common molecular mechanics water models},
journal = {Journal of Chemical Physics},
volume = {132},
pages = {134508},
year = {2005},
type = {Journal Article}
}
%@article{Sindhikara2009,
author = {Sindhikara, Daniel J. and Kim, Seonah and Voter,
Arthur F. and Roitberg, Adrian E.},
title = {{Bad Seeds Sprout Perilous Dynamics: Stochastic
Thermostat Induced Trajectory Synchronization in
Biomolecules}},
journal = {Journal of Chemical Theory and Computation},
year = 2009,
volume = 5,
number = 6,
pages = {1624--1631},
month = {April},
}
%@article{Srinivasan1999,
author = {Srinivasan, J and Trevathan, M. W. and Beroza, P. and Case, D. A.},
title = {Application of a pairwise generalized {Born} model to proteins and nucleic acids: inclusion of salt effects},
journal = {Theor. Chem. Acc.},
volume = {101},
pages = {426-434},
year = {1999},
type = {Journal Article}
}
%@article{Thole1981,
author = {Thole, B. T.},
title = {Molecular polarizabilities calculated with a modified dipole interaction},
journal = {Chemical Physics},
volume = {59},
number = {3},
pages = {341-350},
year = {1981},
type = {Journal Article}
}
%@misc{Tinker,
author = {Ponder, Jay W.},
title = {{TINKER - Software Tools for Molecular Design, 4.2}},
year = {2004}
}
%@article{Uberuaga2004,
author = {Blas P. Uberuaga and Marian Anghel and Arthur
F. Voter},
title = {{Synchronization of trajectories in canonical
molecular-dynamics simulations: observation,
explanation, and exploitation}},
journal = {Journal of Chemical Physics},
year = 2004,
key = {synchronization, parallelization},
volume = 120,
number = 14,
pages = {6363--6374},
}
%@article{Wang2000,
author = {Wang, J. and Cieplak, P. and Kollman, P.A.},
title = {How well does a restrained electrostatic potential ({RESP}) model perform in calculating conformational energies of organic and biological molecules?},
journal = {Journal of Computational Chemistry},
volume = {21},
pages = {1049-1074},
year = {2000},
type = {Journal Article}
}
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