Most (but not all) of these papers are written by GROMACS developers. The papers are listed here solely for your convience in finding references.

• H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R. van Drunen, D. van der Spoel, A. Sijbers, H. Keegstra, B. Reitsma and M.K.R. Renardus: Gromacs: A parallel computer for molecular dynamics simulations. In Physics Computing 92 (Singapore, 1993). R.A. de Groot and J. Nadrchal, eds. . World Scientific.

• H.J.C. Berendsen, D. van der Spoel and R. van Drunen: GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 pp. 43-56 (1995). Abstract. Full text.
  

• E. Lindahl, B. Hess and D. van der Spoel: GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 pp. 306-317 (2001). Abstract. Full text.

• D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen: GROMACS: Fast, Flexible and Free, J. Comp. Chem. 26 pp. 1701-1718 (2005). Abstract. Full text.
• C. Kutzner, D. van der Spoel, M. Fechner,  Erik Lindahl, Udo W. Schmitt, Bert L. de Groot and Helmut Grubmuller Improved GROMACS scaling on Ethernet switched clusters LECTURE NOTES IN COMPUTER SCIENCE 4192: 404-405 (2006)
• A.H. Poghosyan, G.A. Yeghiazaryan, H.H. Charabekyan, A.A. Shahinyan The GROMACS and NAMD software packages comparison Comm. Comp. Phys. 1: 736-743 (2006)
• O.E. Lange, L.V. Schafer and H. Grubmuller Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics J. Comp. Chem. 27: 1693-1702  (2006)
• R.A. Lippert, K. J. Bowers, R. O. Dror , M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary  and D.E. Shaw A common, avoidable source of error in molecular dynamics integrators J. Chem.  Phys. 126: Art. No. 046101 (2007)

• Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Speeding up parallel GROMACS on high-latency networks J. Comp. Chem 28 pp. 2075-2084 (2007)
• Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theor. Comp. 4 pp. 0 (2008)