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Merge pull request #765 from swails/stochastic-forces 

Make it so that random forces and integrators generate unique seeds each time a Context is made
parents 9972e293 df99352d
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docs-source/usersguide/references.bib
View file @ 923ccea5
@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{Berendsen1987
author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
title = {The missing term in effective pair potentials},
journal = {Journal of Physical Chemistry},
volume = {91},
pages = {6269-6271},
year = {1987},
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{Essmann1995
author = {Essmann, Ulrich and Perera, Lalith and Berkowitz, Max L. and Darden, Tom and Lee, Hsing and Pedersen, Lee G.},
title = {A smooth particle mesh {Ewald} method},
journal = {Journal of Chemical Physics},
volume = {103},
number = {19},
pages = {8577-8593},
year = {1995},
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{Hawkins1995
author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.},
title = {Pairwise solute descreening of solute charges from a dielectric medium},
journal = {Chemical Physics Letters},
volume = {246},
number = {1-2},
pages = {122-129},
year = {1995},
type = {Journal Article}
}
@article{Horn2004
author = {Horn, Hans W. and Swope, William C. and Pitera, Jed W. and Madura, Jeffry D. and Dick, Thomas J. and Hura, Greg L. and Head-Gordon, Teresa},
title = {Development of an improved four-site water model for biomolecular simulations: {TIP4P-Ew}},
journal = {Journal of Chemical Physics},
volume = {120},
pages = {9665-9678},
year = {2004},
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}
}
@article{Jorgensen1983
author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.},
title = {Comparison of simple potential functions for simulating liquid water},
journal = {Journal of Chemical Physics},
volume = {79},
pages = {926-935},
year = {1983},
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{Lamoureux2006
author = {Lamoureux, Guillaume and Harder, Edward and Vorobyov, Igor V. and Roux, Benoit and MacKerell Jr., Alexander D.},
title = {A polarizable model of water for molecular dynamics simulations of biomolecules},
journal = {Chemical Physics Letters},
volume = {418},
number = {1-3},
pages = {245-249},
year = {2006},
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{Mahoney2000
author = {Mahoney, Michael W. and Jorgensen, William L.},
title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
journal = {Journal of Chemical Physics},
volume = {112},
pages = {8910-8922},
year = {2000},
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{Mongan2007
author = {Mongan, John and Simmerling, Carlos and McCammon, J. Andrew and Case, David A. and Onufriev, Alexey},
title = {Generalized {Born} model with a simple, robust molecular volume correction},
journal = {Journal of Chemical Theory and Computation},
volume = {3},
number = {1},
pages = {156-169},
year = {2007},
type = {Journal Article}
}
@article{Nguyen2013
author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
title = {Improved Generalized {Born} Solvent Model Parameters for Protein Simulations},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {4},
pages = {2020-2034},
year = {2013},
type = {Journal Article}
}
@article{Onufriev2004
author = {Onufriev, Alexey and Bashford, Donald and Case, David A.},
title = {Exploring protein native states and large-scale conformational changes with a modified generalized {Born} model},
journal = {Proteins},
volume = {55},
number = {22},
pages = {383-394},
year = {2004},
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}
}
@misc{Ponder
author = {Ponder, Jay W.},
title = {Personal communication},
type = {Personal Communication}
}
@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{Schaefer1998
author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin},
title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model},
journal = {Journal of Molecular Biology},
volume = {284},
number = {3},
pages = {835-848},
year = {1998},
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{Shirts2008
author = {Shirts, Michael R. and Chodera, John D.},
title = {Statistically optimal analysis of samples from multiple equilibrium states},
journal = {Journal of Chemical Physics},
volume = {129},
pages = {124105},
year = {2008},
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{Shirts2007
author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
journal = {Journal of Physical Chemistry B},
volume = {111},
pages = {13052-13063},
year = {2007},
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{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{Tironi1995
author = {Tironi, Ilario G. and Sperb, René and Smith, Paul E. and van Gunsteren, Wilfred F.},
title = {A generalized reaction field method for molecular dynamics simulations},
journal = {Journal of Chemical Physics},
volume = {102},
number = {13},
pages = {5451-5459},
year = {1995},
type = {Journal Article}
}
@article{Toukmaji1996
author = {Toukmaji, Abdulnour Y. and Board Jr, John A.},
title = {{Ewald} summation techniques in perspective: a survey},
journal = {Computer Physics Communications},
volume = {95},
pages = {73-92},
year = {1996},
type = {Journal Article}
}
@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}
}
@article{Wang2014
author = {Wang, Lee-Ping and Martinez, Todd J. and Pande, Vijay S.},
title = {Building force fields: an automatic, systematic, and reproducible approach},
journal = {Journal of Physical Chemistry Letters},
volume = {5},
pages = {1885-1891},
year = {2014},
type = {Journal Article}
}
@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{Berendsen1987
author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
title = {The missing term in effective pair potentials},
journal = {Journal of Physical Chemistry},
volume = {91},
pages = {6269-6271},
year = {1987},
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{Essmann1995
author = {Essmann, Ulrich and Perera, Lalith and Berkowitz, Max L. and Darden, Tom and Lee, Hsing and Pedersen, Lee G.},
title = {A smooth particle mesh {Ewald} method},
journal = {Journal of Chemical Physics},
volume = {103},
number = {19},
pages = {8577-8593},
year = {1995},
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{Hawkins1995
author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.},
title = {Pairwise solute descreening of solute charges from a dielectric medium},
journal = {Chemical Physics Letters},
volume = {246},
number = {1-2},
pages = {122-129},
year = {1995},
type = {Journal Article}
}
@article{Horn2004
author = {Horn, Hans W. and Swope, William C. and Pitera, Jed W. and Madura, Jeffry D. and Dick, Thomas J. and Hura, Greg L. and Head-Gordon, Teresa},
title = {Development of an improved four-site water model for biomolecular simulations: {TIP4P-Ew}},
journal = {Journal of Chemical Physics},
volume = {120},
pages = {9665-9678},
year = {2004},
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}
}
@article{Jorgensen1983
author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.},
title = {Comparison of simple potential functions for simulating liquid water},
journal = {Journal of Chemical Physics},
volume = {79},
pages = {926-935},
year = {1983},
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{Lamoureux2006
author = {Lamoureux, Guillaume and Harder, Edward and Vorobyov, Igor V. and Roux, Benoit and MacKerell Jr., Alexander D.},
title = {A polarizable model of water for molecular dynamics simulations of biomolecules},
journal = {Chemical Physics Letters},
volume = {418},
number = {1-3},
pages = {245-249},
year = {2006},
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{Mahoney2000
author = {Mahoney, Michael W. and Jorgensen, William L.},
title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
journal = {Journal of Chemical Physics},
volume = {112},
pages = {8910-8922},
year = {2000},
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{Mongan2007
author = {Mongan, John and Simmerling, Carlos and McCammon, J. Andrew and Case, David A. and Onufriev, Alexey},
title = {Generalized {Born} model with a simple, robust molecular volume correction},
journal = {Journal of Chemical Theory and Computation},
volume = {3},
number = {1},
pages = {156-169},
year = {2007},
type = {Journal Article}
}
@article{Nguyen2013
author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
title = {Improved Generalized {Born} Solvent Model Parameters for Protein Simulations},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {4},
pages = {2020-2034},
year = {2013},
type = {Journal Article}
}
@article{Onufriev2004
author = {Onufriev, Alexey and Bashford, Donald and Case, David A.},
title = {Exploring protein native states and large-scale conformational changes with a modified generalized {Born} model},
journal = {Proteins},
volume = {55},
number = {22},
pages = {383-394},
year = {2004},
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}
}
@misc{Ponder
author = {Ponder, Jay W.},
title = {Personal communication},
type = {Personal Communication}
}
@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{Schaefer1998
author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin},
title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model},
journal = {Journal of Molecular Biology},
volume = {284},
number = {3},
pages = {835-848},
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docs-source/usersguide/theory.rst
View file @ 923ccea5
......@@ -1379,3 +1379,67 @@ specific types of rules. They are:
.. math::
\mathbf{r}=\mathbf{o}+p_1\mathbf{\hat{x}}+p_2\mathbf{\hat{y}}+p_3\mathbf{\hat{z}}
..
Random Numbers with Stochastic Integrators and Forces
*****************************************************
OpenMM includes many stochastic integrators and forces that make extensive use
of random numbers. It is impossible to generate truly random numbers on a
computer like you would with a dice roll or coin flip in real life---instead
programs rely on pseudo-random number generators (PRNGs) that take some sort of
initial "seed" value and steps through a sequence of seemingly random numbers.
The exact implementation of the PRNGs is not important (in fact, each platform
may have its own PRNG whose performance is optimized for that hardware). What
*is* important, however, is that the PRNG must generate a uniform distribution
of random numbers between 0 and 1. Random numbers drawn from this distribution
can be manipulated to yield random integers in a desired range or even a random
number from a different type of probability distribution function (e.g., a
normal distribution).
What this means is that the random numbers used by integrators and forces within
OpenMM cannot have any discernible pattern to them. Patterns can be induced in
PRNGs in two principal ways:
1. The PRNG uses a bad algorithm with a short period.
2. Two PRNGs are started using the same seed
All PRNG algorithms in common use are periodic---that is their sequence of
random numbers repeats after a given *period*, defined by the number of "unique"
random numbers in the repeating pattern. As long as this period is longer than
the total number of random numbers your application requires (preferably by
orders of magnitude), the first problem described above is avoided. All PRNGs
employed by OpenMM have periods far longer than any current simulation can cycle
through.
Point two is far more common in biomolecular simulation, and can result in very
strange artifacts that may be difficult to detect. For example, with Langevin
dynamics, two simulations that use the same sequence of random numbers appear to
synchronize in their global movements.\ :cite:`Uberuaga2004`\
:cite:`Sindhikara2009` It is therefore very important that the stochastic forces
and integrators in OpenMM generate unique sequences of pseudo-random numbers not
only within a single simulation, but between two different simulations of the
same system as well (including any restarts of previous simulations).
Every stochastic force and integrator that does (or could) make use of random
numbers has two instance methods attached to it: :meth:`getRandomNumberSeed()`
and :meth:`setRandomNumberSeed(int seed)`. If you set a unique random seed for
two different simulations (or different forces/integrators if applicable),
OpenMM guarantees that the generated sequences of random numbers will be
different (by contrast, no guarantee is made that the same seed will result in
identical random number sequences).
Since breaking simulations up into pieces and/or running multiple replicates of
a system to obtain more complete statistics is common practice, a new strategy
has been employed for OpenMM versions 6.3 and later with the aim of trying to
ensure that each simulation will be started with a unique random seed. A random
seed value of 0 (the default) will cause a unique random seed to be generated
when a new :class:`Context` is instantiated.
Prior to the introduction of this feature, deserializing a serialized
:class:`System` XML file would result in each stochastic force or integrator
being assigned the same random seed as the original instance that was
serialized. If you use a :class:`System` XML file generated by a version of
OpenMM older than 6.3 to start a new simulation, you should manually set the
random number seed of each stochastic force or integrator to 0 (or another
unique value).
openmmapi/include/openmm/AndersenThermostat.h
View file @ 923ccea5
......@@ -35,6 +35,7 @@
#include "Force.h"
#include <string>
#include "internal/windowsExport.h"
#include "openmm/internal/OSRngSeed.h"
namespace OpenMM {
......@@ -113,6 +114,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/BrownianIntegrator.h
View file @ 923ccea5
......@@ -99,6 +99,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/CustomIntegrator.h
View file @ 923ccea5
......@@ -444,6 +444,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/LangevinIntegrator.h
View file @ 923ccea5
......@@ -99,6 +99,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h
View file @ 923ccea5
......@@ -167,6 +167,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/MonteCarloBarostat.h
View file @ 923ccea5
......@@ -123,6 +123,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/MonteCarloMembraneBarostat.h
View file @ 923ccea5
......@@ -220,6 +220,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/VariableLangevinIntegrator.h
View file @ 923ccea5
......@@ -121,6 +121,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/src/AndersenThermostat.cpp
View file @ 923ccea5
......@@ -37,7 +37,7 @@ using namespace OpenMM;
AndersenThermostat::AndersenThermostat(double defaultTemperature, double defaultCollisionFrequency) :
defaultTemp(defaultTemperature), defaultFreq(defaultCollisionFrequency) {
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
ForceImpl* AndersenThermostat::createImpl() const {
......
openmmapi/src/BrownianIntegrator.cpp
View file @ 923ccea5
......@@ -33,7 +33,6 @@
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/kernels.h"
#include <string>
......@@ -46,7 +45,7 @@ BrownianIntegrator::BrownianIntegrator(double temperature, double frictionCoeff,
setFriction(frictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
void BrownianIntegrator::initialize(ContextImpl& contextRef) {
......
openmmapi/src/CustomIntegrator.cpp
View file @ 923ccea5
......@@ -34,7 +34,6 @@
#include "openmm/OpenMMException.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/kernels.h"
#include <set>
#include <string>
......@@ -45,7 +44,7 @@ using namespace std;
CustomIntegrator::CustomIntegrator(double stepSize) : globalsAreCurrent(true), forcesAreValid(false) {
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
kineticEnergy = "m*v*v/2";
}
......
openmmapi/src/LangevinIntegrator.cpp
View file @ 923ccea5
......@@ -33,7 +33,6 @@
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/kernels.h"
#include <string>
......@@ -46,7 +45,7 @@ LangevinIntegrator::LangevinIntegrator(double temperature, double frictionCoeff,
setFriction(frictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
void LangevinIntegrator::initialize(ContextImpl& contextRef) {
......
openmmapi/src/MonteCarloAnisotropicBarostat.cpp
View file @ 923ccea5
......@@ -31,13 +31,12 @@
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/internal/MonteCarloAnisotropicBarostatImpl.h"
#include "openmm/internal/OSRngSeed.h"
using namespace OpenMM;
MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
defaultPressure(defaultPressure), temperature(temperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
ForceImpl* MonteCarloAnisotropicBarostat::createImpl() const {
......
openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp
View file @ 923ccea5
......@@ -31,6 +31,7 @@
#include "openmm/internal/MonteCarloAnisotropicBarostatImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/Context.h"
#include "openmm/kernels.h"
#include <cmath>
......@@ -60,7 +61,10 @@ void MonteCarloAnisotropicBarostatImpl::initialize(ContextImpl& context) {
numAttempted[i] = 0;
numAccepted[i] = 0;
}
init_gen_rand(owner.getRandomNumberSeed(), random);
int randSeed = owner.getRandomNumberSeed();
// A random seed of 0 means use a unique one
if (randSeed == 0) randSeed = osrngseed();
init_gen_rand(randSeed, random);
}
void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context) {
......
openmmapi/src/MonteCarloBarostat.cpp
View file @ 923ccea5
......@@ -31,13 +31,12 @@
#include "openmm/MonteCarloBarostat.h"
#include "openmm/internal/MonteCarloBarostatImpl.h"
#include "openmm/internal/OSRngSeed.h"
using namespace OpenMM;
MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double temperature, int frequency) :
defaultPressure(defaultPressure), temperature(temperature), frequency(frequency) {
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
ForceImpl* MonteCarloBarostat::createImpl() const {
......
openmmapi/src/MonteCarloBarostatImpl.cpp
View file @ 923ccea5
......@@ -31,6 +31,7 @@
#include "openmm/internal/MonteCarloBarostatImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/Context.h"
#include "openmm/kernels.h"
#include <cmath>
......@@ -58,7 +59,10 @@ void MonteCarloBarostatImpl::initialize(ContextImpl& context) {
volumeScale = 0.01*volume;
numAttempted = 0;
numAccepted = 0;
init_gen_rand(owner.getRandomNumberSeed(), random);
int randSeed = owner.getRandomNumberSeed();
// A random seed of 0 means use a unique one
if (randSeed == 0) randSeed = osrngseed();
init_gen_rand(randSeed, random);
}
void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
......
openmmapi/src/MonteCarloMembraneBarostat.cpp
View file @ 923ccea5
......@@ -31,14 +31,13 @@
#include "openmm/MonteCarloMembraneBarostat.h"
#include "openmm/internal/MonteCarloMembraneBarostatImpl.h"
#include "openmm/internal/OSRngSeed.h"
using namespace OpenMM;
MonteCarloMembraneBarostat::MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double temperature, XYMode xymode, ZMode zmode, int frequency) :
defaultPressure(defaultPressure), defaultSurfaceTension(defaultSurfaceTension), temperature(temperature),
xymode(xymode), zmode(zmode), frequency(frequency) {
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
ForceImpl* MonteCarloMembraneBarostat::createImpl() const {
......
openmmapi/src/MonteCarloMembraneBarostatImpl.cpp
View file @ 923ccea5
......@@ -31,6 +31,7 @@
#include "openmm/internal/MonteCarloMembraneBarostatImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/Context.h"
#include "openmm/kernels.h"
#include <cmath>
......@@ -60,7 +61,10 @@ void MonteCarloMembraneBarostatImpl::initialize(ContextImpl& context) {
numAttempted[i] = 0;
numAccepted[i] = 0;
}
init_gen_rand(owner.getRandomNumberSeed(), random);
int randSeed = owner.getRandomNumberSeed();
// A random seed of 0 means use a unique one
if (randSeed == 0) randSeed = osrngseed();
init_gen_rand(randSeed, random);
}
void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context) {
......
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