Resolve merge conflicts, small changes from tex linter

Author: justinGilmer

README.md

@@ -18,7 +18,7 @@ The current focus is on MD; Monte Carlo (MC) will be addressed in a separate doc
 
 ## Paper writing as code development
 <!-- This discussion is so that people know how to contribute to your document. -->
-This paper is being developed as a living document, open to changes from the community. You can read more about the concept of writing a paper in the same way one would write software code in the essay ["Paper writing as code development"](https://livecomsjournal.github.io/paper_code.html). If you have comments or suggestions, we welcome them! Please [submit them as issues](https://guides.github.com/features/issues/) to this GitHub repository so they can be recorded and given credit for the contribution. Specific changes can be proposed [via pull requests](https://help.github.com/articles/about-pull-requests/).
+This paper is being developed as a living document, open to changes from the community. You can read more about the concept of writing a paper in the same way one would write software code in the essay ["Paper writing as code development"](https://livecomsjournal.github.io/about/paper_code/). If you have comments or suggestions, we welcome them! Please [submit them as issues](https://guides.github.com/features/issues/) to this GitHub repository so they can be recorded and given credit for the contribution. Specific changes can be proposed [via pull requests](https://help.github.com/articles/about-pull-requests/).
 
 ## List of Released Versions
 <!-- update this when you decide to release a version either by preprint or when submitted to LiveCoMS-->

paper/basic_training.bib

@@ -637,3 +637,181 @@ @article{Onufriev2018
 volume = {8},
 year = {2018}
 }
+
+@article{Dupradeau:2010:Phys.Chem.Chem.Phys.,
+  title = {The {{R}}.{{E}}.{{D}}. Tools: Advances in {{RESP}} and {{ESP}} Charge Derivation and Force Field Library Building},
+  volume = {12},
+  issn = {1463-9084},
+  shorttitle = {The {{R}}.{{E}}.{{D}}. Tools},
+  doi = {10.1039/C0CP00111B},
+  language = {en},
+  number = {28},
+  journal = {Phys. Chem. Chem. Phys.},
+  author = {Dupradeau, Fran{\c c}ois-Yves and Pigache, Adrien and Zaffran, Thomas and Savineau, Corentin and Lelong, Rodolphe and Grivel, Nicolas and Lelong, Dimitri and Rosanski, Wilfried and Cieplak, Piotr},
+  month = jul,
+  year = {2010},
+  pages = {7821-7839},
+}
+
+@book{Frenkel:2001:,
+  edition = {2nd},
+  title = {Understanding {{Molecular Simulation}}: {{From Algorithms}} to {{Applications}}},
+  publisher = {{Academic Press}},
+  author = {Frenkel, Daan and Smit, Berend},
+  year = {2001},
+  file = {/Users/dmobley/Zotero/storage/TBRVA2JX/978-0-12-267351-1.html}
+}
+
+@book{allen_computer_2017,
+  address = {New York, NY},
+  edition = {2},
+  series = {Oxford Science Publications},
+  title = {Computer Simulation of Liquids},
+  publisher = {{Oxford University Press}},
+  author = {Allen, M. P. and Tildesley, D. J.},
+  month = aug,
+  year = {2017}
+}
+
+@book{Tuckerman:2010:,
+  address = {Oxford, New York},
+  series = {Oxford Graduate Texts},
+  title = {Statistical {{Mechanics}}: {{Theory}} and {{Molecular Simulation}}},
+  isbn = {978-0-19-852526-4},
+  shorttitle = {Statistical {{Mechanics}}},
+  publisher = {{Oxford University Press}},
+  author = {Tuckerman, Mark E.},
+  month = apr,
+  year = {2010},
+}
+
+@article{Minary:2003:JChemPhys:Algorithms,
+  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},
+  volume={118},
+  number={6},
+  pages={2510--2526},
+  year={2003},
+  publisher={AIP}
+}
+
+@article{Bussi:2007:JChemPhys:Canonical,
+  title={Canonical sampling through velocity rescaling},
+  author={Bussi, Giovanni and Donadio, Davide and Parrinello, Michele},
+  journal={The Journal of chemical physics},
+  volume={126},
+  number={1},
+  pages={014101},
+  year={2007},
+  publisher={AIP}
+}
+
+@article{Braun:2018:Anomalous,
+  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},
+  year={2018}
+}
+
+@InProceedings{Berne:1999:Molecular,
+  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}
+  isbn={978-3-642-58360-5}
+}
+
+@article{Hopkins:2015:JCTC:Long,
+  title={Long-time-step molecular dynamics through hydrogen mass repartitioning},
+  author={Hopkins, Chad W and Le Grand, Scott and Walker, Ross C and Roitberg, Adrian E},
+  journal={Journal of chemical theory and computation},
+  volume={11},
+  number={4},
+  pages={1864--1874},
+  year={2015},
+  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},
+  series = {Interdisciplinary Applied Mathematics},
+  title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
+  volume = {21},
+  publisher = {{Springer}},
+  author = {Schlick, Tamar},
+  year = {2010}
+}
+
+@article{Mobley:2012:JComputAidedMolDes,
+  title = {Let's Get Honest about Sampling},
+  volume = {26},
+  doi = {10.1007/s10822-011-9497-y},
+  journal = {J Comput Aided Mol Des},
+  author = {Mobley, David L},
+  month = jan,
+  year = {2012},
+  pages = {93-95},
+}
+
+@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}
+}