Merge pull request #723 from peastman/docs

Further documentation updates for 6.2

docs-source/usersguide/application.rst

@@ -366,7 +366,8 @@ molecular topology and atom positions.  Your file need not be called
 :file:`input.pdb`.  Feel free to change this line to specify any file you want,
 though it must contain all of the atoms needed by the force field.
 (More information on how to add missing atoms and residues using OpenMM tools can be found in Chapter :ref:`model-building-and-editing`.)
-Make sure you include the single quotes around the file name.
+Make sure you include the single quotes around the file name.  OpenMM also can load
+files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PDBxFile`.
 ::
 
     forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
@@ -805,8 +806,12 @@ you would type:
 
     forcefield = ForceField('amber99sb.xml', 'amber99_obc.xml')
 
+Note that the GBSA-OBC parameters in these files are those used in TINKER.\ :cite:`Tinker`
+They are designed for use with Amber force fields, but they are different from
+the parameters found in the AMBER application.
+
 If you are running a vacuum simulation, you do not need to specify a water
-model.  The following line specifies the AMBER10 force field and no water model.
+model.  The following line specifies the Amber10 force field and no water model.
 If you try to use it with a PDB file that contains explicit water, it will
 produce an error since no water parameters are defined:
 ::

docs-source/usersguide/references.bib

@@ -11,7 +11,7 @@
 
 @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},
+   title = {Molecular dynamics simulations of water and biomolecules with a {Monte Carlo} constant pressure algorithm},
    journal = {Chemical Physics Letters},
    volume = {384},
    pages = {288-294},
@@ -41,7 +41,7 @@
 
 @article{Chow1995
    author = {Chow, Kim-Hung and Ferguson, David M.},
-   title = {Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling},
+   title = {Isothermal-isobaric molecular dynamics simulations with {Monte Carlo} volume sampling},
    journal = {Computer Physics Communications},
    volume = {91},
    pages = {283-289},
@@ -71,7 +71,7 @@
 
 @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},
+   title = {A smooth particle mesh {Ewald} method},
    journal = {Journal of Chemical Physics},
    volume = {103},
    number = {19},
@@ -103,7 +103,7 @@
 
 @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},
+   title = {Development of an improved four-site water model for biomolecular simulations: {TIP4P-Ew}},
    journal = {Journal of Chemical Physics},
    volume = {120},
    pages = {9665-9678},
@@ -113,7 +113,7 @@
 
 @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},
+   title = {Comparison of multiple {Amber} force fields and development of improved protein backbone parameters},
    journal = {Proteins},
    volume = {65},
    pages = {712-725},
@@ -123,7 +123,7 @@
 
 @article{Izaguirre2010
    author = {Izaguirre, Jesús A. and Sweet, Chris R. and Pande, Vijay S.},
-   title = {Multiscale dynamics of macromolecules using Normal Mode Langevin},
+   title = {Multiscale dynamics of macromolecules using {Normal Mode Langevin}},
    journal = {Pacific Symposium on Biocomputing},
    volume = {15},
    pages = {240-251},
@@ -154,7 +154,7 @@
 
 @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},
+   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},
@@ -176,7 +176,7 @@
 
 @article{Lamoureux2003
    author = {Lamoureux, Guillaume and Roux, Benoit},
-   title = {Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm},
+   title = {Modeling induced polarization with classical {Drude} oscillators: Theory and molecular dynamics simulation algorithm},
    journal = {Journal of Chemical Physics},
    volume = {119},
    number = {6},
@@ -187,7 +187,7 @@
 
 @article{Li2010
    author = {Li, D.W. and Br{\"u}schweiler, R.},
-   title = {NMR-based protein potentials},
+   title = {{NMR}-based protein potentials},
    journal = {Angewandte Chemie International Edition},
    volume = {49},
    pages = {6778-6780},
@@ -197,7 +197,7 @@
 
 @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},
+   title = {Improved side-chain torsion potentials for the {Amber ff99SB} protein force field},
    journal = {Proteins},
    volume = {78},
    pages = {1950-1958},
@@ -207,7 +207,7 @@
 
 @article{Liu1989
    author = {Liu, Dong C. and Nocedal, Jorge},
-   title = {On the Limited Memory BFGS Method For Large Scale Optimization},
+   title = {On the Limited Memory {BFGS} Method For Large Scale Optimization},
    journal = {Mathematical Programming},
    volume = {45},
    pages = {503-528},
@@ -217,7 +217,7 @@
 
 @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},
+    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},
@@ -248,7 +248,7 @@
 
 @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},
+   title = {Generalized {Born} model with a simple, robust molecular volume correction},
    journal = {Journal of Chemical Theory and Computation},
    volume = {3},
    number = {1},
@@ -259,7 +259,7 @@
 
 @article{Nguyen2013
    author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
-   title = {Improved Generalized Born Solvent Model Parameters for Protein Simulations},
+   title = {Improved Generalized {Born} Solvent Model Parameters for Protein Simulations},
    journal = {Journal of Chemical Theory and Computation},
    volume = {9},
    number = {4},
@@ -270,7 +270,7 @@
 
 @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},
+   title = {Exploring protein native states and large-scale conformational changes with a modified generalized {Born} model},
    journal = {Proteins},
    volume = {55},
    number = {22},
@@ -281,7 +281,7 @@
 
 @article{Parrinello1984
    author = {Parrinello, M. and Rahman, A.},
-   title = {Study of an F center in molten KCl},
+   title = {Study of an {F} center in molten {KCl}},
    journal = {Journal of Chemical Physics},
    volume = {80},
    number = {2},
@@ -329,7 +329,7 @@
 
 @article{Schnieders2007
    author = {Schnieders, Michael J. and Ponder, Jay W.},
-   title = {Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum},
+   title = {Polarizable Atomic Multipole Solutes in a Generalized {Kirkwood} Continuum},
    journal = {Journal of Chemical Theory and Computation},
    volume = {3},
    pages = {2083-2097},
@@ -349,7 +349,7 @@
 
 @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},
+   title = {Polarizable Atomic Multipole-Based {AMOEBA} Force Field for Proteins},
    journal = {Journal of Chemical Theory and Computation},
    volume = {9},
    number = {9},
@@ -399,6 +399,12 @@
    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},
@@ -412,7 +418,7 @@
 
 @article{Toukmaji1996
    author = {Toukmaji, Abdulnour Y.  and Board Jr, John A.},
-   title = {Ewald summation techniques in perspective: a survey},
+   title = {{Ewald} summation techniques in perspective: a survey},
    journal = {Computer Physics Communications},
    volume = {95},
    pages = {73-92},
@@ -422,7 +428,7 @@
 
 @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?},
+   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},