Merge branch 'master' into efrembraun

Author: EfremBraun

paper/basic_training.bib

@@ -568,6 +568,49 @@ @article{Piana:2012:PLOSONE
   pages = {e39918},
 }
 
+@book{tuckermanBook,
+  title={Statistical mechanics: theory and molecular simulation},
+  author={Tuckerman, Mark},
+  year={2010},
+  publisher={Oxford university press}
+}
+
+@article{Parrinello1981,
+author = {Parrinello, M. and Rahman, A.},
+doi = {10.1063/1.328693},
+issn = {0021-8979},
+journal = {Journal of Applied Physics},
+month = {dec},
+number = {12},
+pages = {7182--7190},
+title = {{Polymorphic transitions in single crystals: A new molecular dynamics method}},
+url = {http://aip.scitation.org/doi/10.1063/1.328693},
+volume = {52},
+year = {1981}
+}
+
+@article{martyna1994constant,
+  title={Constant pressure molecular dynamics algorithms},
+  author={Martyna, Glenn J and Tobias, Douglas J and Klein, Michael L},
+  journal={The Journal of Chemical Physics},
+  volume={101},
+  number={5},
+  pages={4177--4189},
+  year={1994},
+  publisher={AIP}
+}
+
+@article{martyna1996explicit,
+  title={Explicit reversible integrators for extended systems dynamics},
+  author={Martyna, Glenn J and Tuckerman, Mark E and Tobias, Douglas J and Klein, Michael L},
+  journal={Molecular Physics},
+  volume={87},
+  number={5},
+  pages={1117--1157},
+  year={1996},
+  publisher={Taylor \& Francis}
+}
+
 @article{Vega2011,
 author = {Vega, Carlos and Abascal, Jose L.F.},
 doi = {10.1039/c1cp22168j},
@@ -672,19 +715,19 @@ @article{Braun:2018:Anomalous
 }
 
 @InProceedings{Berne:1999:Molecular,
-  author={Berne, Bruce J.}
+  author={Berne, Bruce J.},
   editor={Deuflhard, Peter
   and Hermans, Jan
   and Leimkuhler, Benedict
   and Mark, Alan E.
   and Reich, Sebastian
-  and Skeel, Robert D.}
-  title={Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms}
-  booktitle={Computational Molecular Dynamics: Challenges, Methods, Ideas}
-  year={1999}
-  publisher={Springer}
-  address={Berlin}
-  pages={297--317}
+  and Skeel, Robert D.},
+  title={Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms},
+  booktitle={Computational Molecular Dynamics: Challenges, Methods, Ideas},
+  year={1999},
+  publisher={Springer},
+  address={Berlin},
+  pages={297--317},
   isbn={978-3-642-58360-5}
 }
 
@@ -699,6 +742,13 @@ @article{Hopkins:2015:JCTC:Long
   publisher={ACS Publications}
 }
 
+@book{ShellBook, 
+ author = "Shell, M. Scott",
+ title = "Thermodynamics and Statistical Mechanics: An Integrated Approach",
+ year = "2015",
+ publisher = "Cambridge University Press"
+} 
+
 @book{Schlick:2010:,
   address = {New York},
   edition = {2},
@@ -720,3 +770,123 @@ @article{Mobley:2012:JComputAidedMolDes
   year = {2012},
   pages = {93-95},
 }
+
+@book{Reif:2008:,
+  title = {Fundamentals of {{Statistical}} and {{Thermal Physics}}},
+  publisher = {{Waveland Press}},
+  author = {Reif, Frederick},
+  year = {2008}
+}
+
+@book{McQuarrie:2000:,
+  title = {Statistical {{Mechanics}}},
+  publisher = {{University Science Books}},
+  author = {McQuarrie, Donald A.},
+  year = {2000}
+}
+
+@book{Hill:1987:,
+  title = {Statistical {{Mechanics}}: {{Principles}} and {{Selected Applications}}},
+  publisher = {{Dover Publications}},
+  author = {Hill, Terrell L.},
+  year = {1987}
+}
+
+@book{Chandler:1987:,
+  title = {Introduction to {{Modern Statistical Mechanics}}},
+  publisher = {{Oxford University Press}},
+  author = {Chandler, David},
+  month = sep,
+  year = {1987}
+}
+
+@book{Griffiths:2017:,
+  edition = {4th},
+  title = {Introduction to {{Electrodynamics}}},
+  publisher = {{Cambridge University Press}},
+  author = {Griffiths, David J.},
+  month = jul,
+  year = {2017}
+}
+
+@book{Jackson:1998:,
+  edition = {3rd},
+  title = {Classical {{Electrodynamics}}},
+  publisher = {{Wiley}},
+  author = {Jackson, John David},
+  year = {1998}
+}
+
+@book{McQuarrie:1997:,
+  title = {Phyysical {{Chemistry}}: {{A Molecular Approach}}},
+  publisher = {{University Science Books}},
+  author = {McQuarrie, Donald A. and Simon, John D.},
+  month = jul,
+  year = {1997}
+}
+
+@book{Kittel:1980:,
+  edition = {2nd},
+  title = {Thermal {{Physics}}},
+  publisher = {{W. H. Freeman}},
+  author = {Kittel, Charles and Kroemer, Herbert},
+  month = jan,
+  year = {1980}
+}
+
+@article{Fass2018,
+author = {Fass, Josh and Sivak, David and Crooks, Gavin E and Beauchamp, Kyle A and Leimkuhler, Benedict and Chodera, John},
+doi = {10.1101/266619},
+issn = {1099-4300},
+journal = {bioRxiv},
+number = {1},
+pages = {266619},
+title = {{Quantifying configuration-sampling error in Langevin simulations of complex molecular systems}},
+url = {https://www.biorxiv.org/content/early/2018/03/31/266619},
+year = {2018}
+}
+
+@article{Tuckerman:1992:,
+author = {Tuckerman, M and Berne, B J and Martyna, G J},
+doi = {10.1063/1.463137},
+journal = {The Journal of Chemical Physics},
+number = {3},
+pages = {1990--2001},
+title = {{Reversible multiple time scale molecular dynamics}},
+volume = {97},
+year = {1992}
+}
+
+@article{GonzalezSalgado2010,
+author = {{Gonzalez Salgado}, D. and Vega, C.},
+doi = {10.1063/1.3328667},
+journal = {Journal of Chemical Physics},
+number = {9},
+pmid = {20210403},
+title = {{Melting point and phase diagram of methanol as obtained from computer simulations of the OPLS model}},
+volume = {132},
+year = {2010}
+}
+
+@article{Kofke1993,
+author = {Kofke, David A.},
+doi = {10.1063/1.465023},
+journal = {The Journal of Chemical Physics},
+number = {5},
+pages = {4149--4162},
+title = {{Direct evaluation of phase coexistence by molecular simulation via integration along the saturation line}},
+volume = {98},
+year = {1993}
+}
+
+@article{Shirts:2007:JPhysChemB,
+  title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations.},
+  volume = {111},
+  doi = {10.1021/jp0735987},
+  number = {45},
+  journal = {J Phys Chem B},
+  author = {Shirts, Michael R and Mobley, David L and Chodera, John D and Pande, Vijay S},
+  month = nov,
+  year = {2007},
+  pages = {13052-13063},
+}