2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
39 #include "pleasecite.h"
43 #include "gromacs/utility/arraysize.h"
44 #include "gromacs/utility/baseversion.h"
45 #include "gromacs/utility/cstringutil.h"
46 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/utility/stringutil.h"
58 void please_cite(FILE *fp, const char *key)
60 static const t_citerec citedb[] = {
62 "M. P. Allen and D. J. Tildesley",
63 "Computer simulation of liquids",
64 "Oxford Science Publications",
67 "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
68 "GROMACS: A message-passing parallel molecular dynamics implementation",
72 "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
73 "Molecular dynamics with coupling to an external bath",
75 81, 1984, "3684-3690" },
77 "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
78 "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
80 23, 1977, "327-341" },
82 "S. Miyamoto and P. A. Kollman",
83 "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
85 13, 1992, "952-962" },
87 "D. T. Cromer & J. B. Mann",
88 "X-ray scattering factors computed from numerical Hartree-Fock wave functions",
92 "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
93 "Algorithms for Constrained Molecular Dynamics",
95 16, 1995, "1192-1209" },
97 "U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
98 "A smooth particle mesh Ewald method",
100 103, 1995, "8577-8592" },
102 "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
103 "Time-dependent distance restraints in molecular dynamics simulations",
105 157, 1989, "289-294" },
107 "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
108 "Generalized reaction field method for molecular dynamics simulations",
110 102, 1995, "5451-5459" },
112 "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
113 "LINCS: A Linear Constraint Solver for molecular simulations",
115 18, 1997, "1463-1472" },
118 "P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
119 "J. Chem. Theory Comput.",
120 4, 2008, "116-122" },
122 "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
123 "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
124 "J. Chem. Theory Comput.",
125 4, 2008, "435-447" },
127 "J. S. Hub, B. L. de Groot and D. van der Spoel",
128 "g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates",
129 "J. Chem. Theory Comput.",
130 6, 2010, "3713-3720"},
132 "Y. In-Chul and M. L. Berkowitz",
133 "Ewald summation for systems with slab geometry",
135 111, 1999, "3155-3162" },
137 "B. L. de Groot and D. M. F. van Aalten and R. M. Scheek and A. Amadei and G. Vriend and H. J. C. Berendsen",
138 "Prediction of Protein Conformational Freedom From Distance Constrains",
140 29, 1997, "240-251" },
142 "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
143 "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
145 108, 1998, "10220-10230" },
147 "D. S. Wishart and A. M. Nip",
148 "Protein Chemical Shift Analysis: A Practical Guide",
149 "Biochem. Cell Biol.",
150 76, 1998, "153-163" },
152 "V. N. Maiorov and G. M. Crippen",
153 "Size-Independent Comparison of Protein Three-Dimensional Structures",
154 "PROTEINS: Struct. Funct. Gen.",
155 22, 1995, "273-283" },
157 "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
158 "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
160 20, 1999, "786-798" },
162 "Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David van der Spoel and Luciano T. Costa",
163 "Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View",
164 "Environ. Sci. Technol.",
165 47, 2013, "7421-7429" },
167 "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
168 "Auger Electron Cascades in Water and Ice",
170 299, 2004, "277-283" },
172 "T. A. Pascal and S. T. Lin and W. A. Goddard III",
173 "Thermodynamics of liquids: standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics",
174 "Phys. Chem. Chem. Phys.",
175 13, 2011, "169-181" },
177 "C. Caleman and D. van der Spoel",
178 "Picosecond Melting of Ice by an Infrared Laser Pulse: A Simulation Study",
179 "Angew. Chem. Int. Ed",
180 47, 2008, "1417-1420" },
182 "C. Caleman and P. J. van Maaren and M. Hong and J. S. Hub and L. T. da Costa and D. van der Spoel",
183 "Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant",
184 "J. Chem. Theo. Comp.",
187 "E. Lindahl and B. Hess and D. van der Spoel",
188 "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
190 7, 2001, "306-317" },
192 "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
193 "Solvation model based on weighted solvent accessible surface area",
195 105, 2001, "5055-5067" },
197 "D. Eisenberg and A. D. McLachlan",
198 "Solvation energy in protein folding and binding",
200 319, 1986, "199-203" },
203 "van der Waals Volumes and Radii",
205 68, 1964, "441-451" },
207 "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
208 "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
210 16, 1995, "273-284" },
212 "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
213 "Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
215 116, 2002, "9602-9610" },
217 "B. Hess and R.M. Scheek",
218 "Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
220 164, 2003, "19-27" },
222 "A. K. Rappe and W. A. Goddard III",
223 "Charge Equillibration for Molecular Dynamics Simulations",
225 95, 1991, "3358-3363" },
227 "Y. Mu, P. H. Nguyen and G. Stock",
228 "Energy landscape of a small peptide revelaed by dihedral angle principal component analysis",
229 "Prot. Struct. Funct. Bioinf.",
232 "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
233 "Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
235 335, 2001, "435-439" },
237 "K. Hukushima and K. Nemoto",
238 "Exchange Monte Carlo Method and Application to Spin Glass Simulations",
239 "J. Phys. Soc. Jpn.",
240 65, 1996, "1604-1608" },
243 "Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances",
245 72, 1980, "6035-6043" },
247 "P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. Waroquier and J. P. Tollenaere",
248 "The electronegativity equalization method I: Parametrization and validation for atomic charge calculations",
250 106, 2002, "7887-7894" },
252 "Q. Y. Yang and K. A. Sharp",
253 "Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization",
254 "J. Chem. Theory Comput.",
255 2, 2006, "1152-1167" },
257 "D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
258 "GROMACS: Fast, Flexible and Free",
260 26, 2005, "1701-1719" },
262 "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
263 "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
265 110, 2006, "4393-4398" },
267 "D. van der Spoel and M. M. Seibert",
268 "Protein folding kinetics and thermodynamics from atomistic simulations",
269 "Phys. Rev. Letters",
270 96, 2006, "238102" },
273 "Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids",
275 49, 1994, "359-366" },
277 "G. Bussi, D. Donadio and M. Parrinello",
278 "Canonical sampling through velocity rescaling",
280 126, 2007, "014101" },
282 "J. S. Hub and B. L. de Groot",
283 "Does CO2 permeate through Aquaporin-1?",
285 91, 2006, "842-848" },
287 "J. S. Hub and B. L. de Groot",
288 "Mechanism of selectivity in aquaporins and aquaglyceroporins",
290 105, 2008, "1198-1203" },
292 "M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, and V. S. Pande",
293 "Accelerating Molecular Dynamic Simulation on Graphics Processing Units",
295 30, 2009, "864-872" },
297 "O. Engin, A. Villa, M. Sayar and B. Hess",
298 "Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
300 114, 2010, "11093" },
302 "H. Wang, F. Dommert, C.Holm",
303 "Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency",
305 133, 2010, "034117" },
307 "Y. Sugita, Y. Okamoto",
308 "Replica-exchange molecular dynamics method for protein folding",
310 314, 1999, "141-151" },
312 "C. Kutzner and J. Czub and H. Grubmuller",
313 "Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS",
314 "J. Chem. Theory Comput.",
315 7, 2011, "1381-1393" },
317 "M. Hoefling, N. Lima, D. Haenni, C.A.M. Seidel, B. Schuler, H. Grubmuller",
318 "Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach",
322 "R. W. Hockney and J. W. Eastwood",
323 "Computer simulation using particles",
327 "V. Ballenegger, J.J. Cerda, and C. Holm",
328 "How to Convert SPME to P3M: Influence Functions and Error Estimates",
329 "J. Chem. Theory Comput.",
330 8, 2012, "936-947" },
332 "Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
333 "Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament",
334 "Journal of Physics: Conference Series",
335 340, 2012, "012094" },
337 "C. Kutzner, H. Grubmuller, B. L. de Groot, and U. Zachariae",
338 "Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail",
340 101, 2011, "809-817"},
342 "M. Lundborg, R. Apostolov, D. Spangberg, A. Gardenas, D. van der Spoel and E. Lindahl",
343 "An efficient and extensible format, library, and API for binary trajectory data from molecular simulations",
345 35, 2014, "260-269"},
347 "N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C. Berendsen",
348 "Efficient Algorithms for Langevin and DPD Dynamics",
349 "J. Chem. Theory Comput.",
350 8, 2012, "3637--3649"},
352 "S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl",
353 "GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit",
357 "S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl",
358 "Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS",
359 "In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale",
360 8759, 2015, "3-27" },
362 "M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl",
363 "GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers",
367 "V. Ballenegger, A. Arnold, J. J. Cerdà",
368 "Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions",
370 131, 2009, "094107" },
372 "J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof",
373 "Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge",
374 "J. Chem. Theory Comput.",
375 10, 2014, "381-393" },
377 "D. van der Spoel, M. M. Ghahremanpour, J. Lemkul",
378 "Small Molecule Thermochemistry: A Tool For Empirical Force Field Development",
380 122, 2018, "8982-8988" },
382 "V. Lindahl, J. Lidmar, B. Hess",
383 "Accelerated weight histogram method for exploring free energy landscapes",
385 141, 2014, "044110" },
387 #define NSTR static_cast<int>(asize(citedb))
392 #define LINE_WIDTH 79
399 for (index = 0; index < NSTR && (strcmp(citedb[index].key, key) != 0); index++)
404 fprintf(fp, "\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
407 /* Insert newlines */
408 author = wrap_lines(citedb[index].author, LINE_WIDTH, 0, FALSE);
409 title = wrap_lines(citedb[index].title, LINE_WIDTH, 0, FALSE);
410 fprintf(fp, "%s\n%s\n%s %d (%d) pp. %s\n",
411 author, title, citedb[index].journal,
412 citedb[index].volume, citedb[index].year,
413 citedb[index].pages);
419 fprintf(fp, "Entry %s not found in citation database\n", key);
421 fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");
426 writeSourceDoi(FILE *fp)
428 /* Check if we are in release mode or not.
429 * TODO The check should properly target something else than
430 * the string being empty
432 if (strlen(gmxDOI()) == 0)
434 /* Not a release build, return without printing anything */
437 gmx::TextLineWrapper wrapper;
438 wrapper.settings().setLineLength(LINE_WIDTH);
439 wrapper.settings().setFirstLineIndent(0);
440 const std::string doiString = wrapper.wrapToString(gmxDOI());
446 fprintf(fp, "\n++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++\n");
447 fprintf(fp, "%s%s\n", "https://doi.org/", doiString.c_str());
448 fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");