Updated pdf.

Author: JIMonroe

.gitignore

@@ -169,6 +169,7 @@ TSWLatexianTemp*
 # WinEdt
 *.bak
 *.sav
+.idea/
 
 # Texpad
 .texpadtmp

paper/basic_training.bib

@@ -49,13 +49,6 @@ @book{GlodsteinBook
  edition = "Third"
 }
 
-@book{ReifBook,
- author = "Reif, Frederick",
- title = "Fundamentals of Statiscal and Thermal Physics",
- year = "2009",
- publisher = "Waveland Press, Inc."
-}
-
 @book{ZemanskyBook,
  author = "Zemansky, Mark W. and Dittman, Richard H.",
  title = "Heat and Thermodynamics",
@@ -181,18 +174,21 @@ @article{amber15FB
 }
 
 @article{mackerell2004CMAP,
-author = {Mackerell Alexander D. and Feig Michael and Brooks Charles L.},
-title = {Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations},
-journal = {Journal of Computational Chemistry},
-volume = {25},
-number = {11},
-pages = {1400-1415},
-keywords = {ab initio, CMAP, molecular dynamics, dihedral angles, empirical force field, molecular mechanics},
+author = {{Mackerell, Jr.}, Alexander D. and Feig, Michael and {Brooks, III}, Charles L.},
 doi = {10.1002/jcc.20065},
+journal = {J. Comput. Chem.},
+keywords = {ab initio,cmap,dihedral angles,empirical force field,molecular dynamics,molecular mechanics},
+number = {11},
+pages = {1400--1415},
+title = {{Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations}},
 url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20065},
-eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20065}
+volume = {25},
+year = {2004}
 }
 
+
+
+
 @article{perez2015,
 author = {Perez, Alberto and MacCallum, Justin L. and Brini, Emiliano and Simmerling, Carlos and Dill, Ken A.},
 doi = {10.1021/acs.jctc.5b00662},
@@ -297,7 +293,7 @@ @article{Mishra2017
 @article{Lopes2009,
 archivePrefix = {arXiv},
 arxivId = {NIHMS150003},
-author = {Lopes, Pedro E.M. and Roux, Benoit and MacKerell, Alexander D.},
+author = {Lopes, Pedro E.M. and Roux, Benoit and {Mackerell, Jr.}, Alexander D.},
 doi = {10.1007/s00214-009-0617-x},
 eprint = {NIHMS150003},
 file = {:Users/jacobmonroe/Documents/Papers{\_}Library/Best{\_}Practices/Lopes2009{\_}Polarizable{\_}models{\_}review.pdf:pdf},
@@ -377,7 +373,7 @@ @article{Grossfield:2009:AnnuRepComputChem
   pmcid = {PMC2865156}
 }
 
-@article{Zuckerman:2011:Annu.Rev.Biophys.,
+@article{Zuckerman:2011:AnnuRevBiophys,
   title = {Equilibrium {{Sampling}} in {{Biomolecular Simulations}}},
   volume = {40},
   doi = {10.1146/annurev-biophys-042910-155255},
@@ -416,7 +412,7 @@ @misc{Zuckerman:2015:StatisticalBiophysicsBlog
   file = {/Users/dmobley/Zotero/storage/KAQSYA4R/statisticalbiophysicsblog.org.html}
 }
 
-@article{Zuckerman:2017:Annu.Rev.Biophys.,
+@article{Zuckerman:2017:AnnuRevBiophys,
   title = {Weighted {{Ensemble Simulation}}: {{Review}} of {{Methodology}}, {{Applications}}, and {{Software}}},
   volume = {46},
   shorttitle = {Weighted {{Ensemble Simulation}}},
@@ -443,7 +439,7 @@ @book{Zuckerman:2010:
   file = {/Users/dmobley/Zotero/storage/5GL7B76J/9781420073782.html}
 }
 
-@article{Ponder:2010:J.Phys.Chem.B,
+@article{Ponder:2010:JPhysChemB,
   title = {Current {{Status}} of the {{AMOEBA Polarizable Force Field}}},
   volume = {114},
   issn = {1520-6106},
@@ -456,21 +452,21 @@ @article{Ponder:2010:J.Phys.Chem.B
   pages = {2549-2564},
 }
 
-@article{Lemkul:2016:Chem.Rev.,
+@article{Lemkul:2016:ChemRev,
   title = {An {{Empirical Polarizable Force Field Based}} on the {{Classical Drude Oscillator Model}}: {{Development History}} and {{Recent Applications}}},
   volume = {116},
   issn = {0009-2665},
   shorttitle = {An {{Empirical Polarizable Force Field Based}} on the {{Classical Drude Oscillator Model}}},
   doi = {10.1021/acs.chemrev.5b00505},
   number = {9},
   journal = {Chem. Rev.},
-  author = {Lemkul, Justin A. and Huang, Jing and Roux, Beno\^it and MacKerell, Alexander D.},
+  author = {Lemkul, Justin A. and Huang, Jing and Roux, Beno\^it and {Mackerell, Jr.}, Alexander D.},
   month = may,
   year = {2016},
   pages = {4983-5013},
 }
 
-@article{York:1993:J.Chem.Phys.,
+@article{York:1993:JChemPhys,
   title = {The Effect of Long-range Electrostatic Interactions in Simulations of Macromolecular Crystals: {{A}} Comparison of the {{Ewald}} and Truncated List Methods},
   volume = {99},
   issn = {0021-9606, 1089-7690},
@@ -485,7 +481,7 @@ @article{York:1993:J.Chem.Phys.
   pages = {8345-8348},
 }
 
-@article{Darden:1993:J.Chem.Phys.,
+@article{Darden:1993:JChemPhys,
   title = {Particle Mesh {{Ewald}}: {{An N}} Log( {{N}} ) Method for {{Ewald}} Sums in Large Systems},
   volume = {98},
   issn = {0021-9606, 1089-7690},
@@ -500,7 +496,7 @@ @article{Darden:1993:J.Chem.Phys.
   pages = {10089-10092},
 }
 
-@article{Sagui:1999:Annu.Rev.Biophys.Biomol.Struct.,
+@article{Sagui:1999:AnnuRevBiophysBiomolStruct,
   title = {{{MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES}}: {{Long}}-{{Range Electrostatic Effects}}},
   volume = {28},
   shorttitle = {{{MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES}}},
@@ -513,7 +509,7 @@ @article{Sagui:1999:Annu.Rev.Biophys.Biomol.Struct.
   pmid = {10410799}
 }
 
-@article{Cisneros:2014:Chem.Rev.,
+@article{Cisneros:2014:ChemRev,
   title = {Classical {{Electrostatics}} for {{Biomolecular Simulations}}},
   volume = {114},
   issn = {0009-2665, 1520-6890},
@@ -527,7 +523,7 @@ @article{Cisneros:2014:Chem.Rev.
   pages = {779-814},
 }
 
-@article{Basconi:2013:J.Chem.TheoryComput.,
+@article{Basconi:2013:JChemTheoryComput,
   title = {Effects of {{Temperature Control Algorithms}} on {{Transport Properties}} and {{Kinetics}} in {{Molecular Dynamics Simulations}}},
   volume = {9},
   issn = {1549-9618},
@@ -540,7 +536,7 @@ @article{Basconi:2013:J.Chem.TheoryComput.
   pages = {2887-2899},
 }
 
-@article{Shirts:2013:J.Chem.TheoryComput.,
+@article{Shirts:2013:JChemTheoryComput,
   title = {Simple {{Quantitative Tests}} to {{Validate Sampling}} from {{Thermodynamic Ensembles}}},
   volume = {9},
   issn = {1549-9618},
@@ -638,7 +634,7 @@ @article{Onufriev2018
 year = {2018}
 }
 
-@article{Dupradeau:2010:Phys.Chem.Chem.Phys.,
+@article{Dupradeau:2010:PhysChemChemPhys,
   title = {The {{R}}.{{E}}.{{D}}. Tools: Advances in {{RESP}} and {{ESP}} Charge Derivation and Force Field Library Building},
   volume = {12},
   issn = {1463-9084},
@@ -685,7 +681,7 @@ @book{Tuckerman:2010:
   year = {2010},
 }
 
-@article{Minary:2003:JChemPhys:Algorithms,
+@article{Minary:2003:JChemPhysAlgorithms,
   title={Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics},
   author={Minary, Peter and Martyna, Glenn J and Tuckerman, Mark E},
   journal={The Journal of chemical physics},
@@ -707,7 +703,7 @@ @article{Bussi:2007:JChemPhys:Canonical
   publisher={AIP}
 }
 
-@article{Braun:2018:Anomalous,
+@article{Braun:2018,
   title={Anomalous effects of velocity rescaling algorithms: the flying ice cube effect revisited},
   author={Braun, Efrem and Moosavi, Seyed Mohamad and Smit, Berend},
   journal={arXiv preprint arXiv:1805.02295},
@@ -771,11 +767,14 @@ @article{Mobley:2012:JComputAidedMolDes
   pages = {93-95},
 }
 
-@book{Reif:2008:,
-  title = {Fundamentals of {{Statistical}} and {{Thermal Physics}}},
-  publisher = {{Waveland Press}},
-  author = {Reif, Frederick},
-  year = {2008}
+@book{Reif:2009:,
+address = {Long Grove, IL},
+author = {Reif, F.},
+isbn = {1-57766-612-7},
+pages = {651},
+publisher = {Waveland Press, Inc.},
+title = {{Fundamentals of Statistical and Thermal Physics}},
+year = {2009}
 }
 
 @book{McQuarrie:2000:,
@@ -835,15 +834,15 @@ @book{Kittel: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}
+	author = {Fass, Josh and Sivak, David and Crooks, Gavin E. and Beauchamp, Kyle A. and Leimkuhler, Benedict and Chodera, John},
+	title = {Quantifying configuration-sampling error in Langevin simulations of complex molecular systems},
+	year = {2018},
+	doi = {10.1101/266619},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2018/02/16/266619},
+	eprint = {https://www.biorxiv.org/content/early/2018/02/16/266619.full.pdf},
+	journal = {bioRxiv},
+	pages = {266619}
 }
 
 @article{Tuckerman:1992:,
@@ -891,7 +890,7 @@ @article{Shirts:2007:JPhysChemB
   pages = {13052-13063},
 }
 
-@article{Chen:2014:Mol.Simul.,
+@article{Chen:2014:MolSimul,
   title = {Recent Development and Application of Constant {{pH}} Molecular Dynamics},
   volume = {40},
   issn = {0892-7022},
@@ -904,3 +903,71 @@ @article{Chen:2014:Mol.Simul.
   keywords = {pH,molecular dynamics,algorithms,electrostatics,pKa calculation},
   pages = {830-838},
 }
+@article{Towns2014,
+author = {Towns, John and Cockerill, Timothy and Dahan, Maytal and Foster, Ian and Gaither, Kelly and Grimshaw, Andrew and Hazlewood, Victor and Lathrop, Scott and Lifka, Dave and Peterson, Gregory D. and Roskies, Ralph and Scott, J. Ray and Wilkens-Diehr, Nancy},
+doi = {10.1109/MCSE.2014.80},
+issn = {1521-9615},
+journal = {Comput. Sci. Eng.},
+number = {5},
+pages = {62--74},
+title = {{XSEDE: Accelerating Scientific Discovery}},
+url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6866038},
+volume = {16},
+year = {2014}
+}
+@article{Kirchmair2015,
+author = {Kirchmair, Johannes and G{\"{o}}ller, Andreas H. and Lang, Dieter and Kunze, Jens and Testa, Bernard and Wilson, Ian D and Glen, Robert C and Schneider, Gisbert},
+doi = {10.1038/nrd4581},
+issn = {1474-1776},
+journal = {Nat. Rev. Drug Discov.},
+number = {6},
+pages = {387--404},
+publisher = {Nature Publishing Group},
+title = {{Predicting drug metabolism: experiment and/or computation?}},
+url = {http://dx.doi.org/10.1038/nrd4581},
+volume = {14},
+year = {2015}
+}
+@article{Sresht2017,
+author = {Sresht, Vishnu and Lewandowski, Eric P. and Blankschtein, Daniel and Jusuf, Arben},
+doi = {10.1021/acs.langmuir.7b01073},
+journal = {Langmuir},
+pages = {8319−8329},
+title = {{Combined Molecular Dynamics Simulation–Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions}},
+url = {https://pubs.acs.org/doi/abs/10.1021/acs.langmuir.7b01073{\#}},
+volume = {33},
+year = {2017}
+}
+@article{Nussinov2014,
+author = {Nussinov, Ruth},
+doi = {10.1371/journal.pcbi.1003423},
+file = {:Users/hbmayes/bee/literature/MDSuccess/2014Nussinov{\_}Sig2013Nobel.pdf:pdf},
+journal = {PLoS Comput. Biol.},
+mendeley-groups = {**Mobley},
+number = {1},
+pages = {2013--2014},
+title = {{The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead}},
+url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003423},
+volume = {10},
+year = {2014}
+}
+@article{Bottaro2018,
+author = {Bottaro, Sandro and Lindorff-Larsen, Kresten},
+file = {:Users/hbmayes/bee/literature/MDSuccess/2018Bottaro{\_}BioExpSim.pdf:pdf},
+journal = {Science (80-. ).},
+mendeley-groups = {Reference},
+pages = {355--360},
+title = {{Biophysical experiments and biomolecular simulations: A perfect match?}},
+url = {http://science.sciencemag.org/content/361/6400/355/tab-pdf},
+volume = {360},
+year = {2018}
+}
+@book{Jensen2007,
+address = {West Sussex, England},
+author = {Jensen, Frank},
+edition = {Second},
+isbn = {9780470011867},
+publisher = {John Wiley {\&} Sons},
+title = {{Introduction to Computational Chemistry}},
+year = {2007}
+}