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

docs-source/usersguide/references.bib

-@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},
+   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{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{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{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}
+}
+
+@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}
+}

docs-source/usersguide/theory.rst

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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) {