Add GROMACS 5 paper to paper lists

Also call to please_cite, and cite both recent papers
in the reference manual

Change-Id: I5e7a81690a1d0fbea0147d8a2a5f281f7b5d4aab

diff --git a/docs/manual/gromacs.tex b/docs/manual/gromacs.tex
index 8a496e649783c01b8be54c17c80f0cf1bed21a61..198d92da915be5c262d505fdf83b73cc65e9ceb2 100644 (file)
--- a/docs/manual/gromacs.tex
+++ b/docs/manual/gromacs.tex
@@ -1,7 +1,7 @@
 %
 % This file is part of the GROMACS molecular simulation package.
 %
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
 % Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 % and including many others, as listed in the AUTHORS file in the
 % top-level source directory and at http://www.gromacs.org.
@@ -201,7 +201,7 @@ M.J. Abraham, D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development
 \hspace{0.3em} {\wwwpage} ({\gmxyear})
 \end{quote}
 However, we prefer that you cite (some of) the {\gromacs}
-papers~\cite{Bekker93a,Berendsen95a,Lindahl2001a,Spoel2005a,Hess2008b,Pronk2013}
+papers~\cite{Bekker93a,Berendsen95a,Lindahl2001a,Spoel2005a,Hess2008b,Pronk2013,Pall2015,Abraham2015}
 when you publish your results. Any future development depends on academic research
 grants, since the package is distributed as free software!
 

diff --git a/docs/manual/monster.bib b/docs/manual/monster.bib
index 3c14898f4be4dc2ef87ab17ccc77ca0cc7b98dcc..b6e0bf868a87903f2907d66501aefda9dba4e541 100644 (file)
--- a/docs/manual/monster.bib
+++ b/docs/manual/monster.bib
@@ -8691,3 +8691,27 @@ pages = {105--120},
 keywords = {CHARMM, force field, molecular dynamics, parametrization, DNA, RNA},
 year = {2000},
 }
+
+@incollection {Pall2015,
+author = {P{\'a}ll, Szil{\'a}rd and Abraham, Mark James and Kutzner, Carsten and Hess, Berk and Lindahl, Erik},
+title = { Tackling Exascale Software Challenges in Molecular Dynamics Simulati\
+ons with {GROMACS} },
+booktitle = {Solving Software Challenges for Exascale },
+editor = { Markidis, Stephano and Laure, Erwin },
+pages = { 3--27 },
+year = { 2015 },
+volume = { 8759 },
+publisher = { Springer International Publishing Switzerland },
+address = { London }
+}
+
+@article {Abraham2015,
+author = { Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{\'a}ll, Szil{\'a}rd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik },
+title = { {GROMACS}: High performance molecular simulations through multi-level parallelism from laptops to supercomputers },
+journal = { {SoftwareX} },
+volume = { 1--2 },
+publisher = { John Wiley & Sons, Inc. },
+pages = { 19--25 },
+year = { 2015 },
+doi = "http://dx.doi.org/10.1016/j.softx.2015.06.001"
+}

diff --git a/src/gromacs/gmxlib/copyrite.cpp b/src/gromacs/gmxlib/copyrite.cpp
index fc2df6efd1cf6299627016a69d30f636268cda18..d282d218c26e7ee31502100a1acf0554e1337a0e 100644 (file)
--- a/src/gromacs/gmxlib/copyrite.cpp
+++ b/src/gromacs/gmxlib/copyrite.cpp
@@ -581,7 +581,12 @@ void please_cite(FILE *fp, const char *key)
           "S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl",
           "Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS",
           "In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale",
-          8759, 2015, "3-27" }
+          8759, 2015, "3-27" },
+        { "Abraham2015",
+          "M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl",
+          "GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers",
+          "SoftwareX",
+          1, 2015, "19-25" },
     };
 #define NSTR (int)asize(citedb)
 

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index ee2806226522a9d471111c6eccccdd6091a6dc6f..e3571f634057cc40debe673695b4da6287b95e13 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -762,6 +762,7 @@ int gmx_mdrun(int argc, char *argv[])
     {
         gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
                      !bSepPot, Flags & MD_APPENDFILES, &fplog);
+        please_cite(fplog, "Abraham2015");
         please_cite(fplog, "Pall2015");
         please_cite(fplog, "Pronk2013");
         please_cite(fplog, "Hess2008b");