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. 2016 May 24;6:26536. doi: 10.1038/srep26536

Figure 1. Development of molecular dynamics over the past decades.

Figure 1

(A) Number of MD papers per year since 1975. The value was calculated using the search term “molecular dynamics” in Thomson Reuters Web of Science, where we filtered the number of publications per year that present MD as a research topic. The curve shows a substantial evolution of MD simulation over the years, even though our search term is likely excluding many publications that present MD results. (B) Evolution of the usage of some of the most employed MD tools today. Visual Molecular Dynamics (VMD) is also included as it is one of the most employed set-up and analysis tools. The plot shows the number of citations (Google Scholar) of these programs’ main publications per year. We considered 2 publications for NAMD; 5 for GROMACS; 3 for AMBER; 1 for LAMPS; 2 for CHARMM; and 1 for VMD. The list of publications employed is presented in Supplementary Note S1. The plots show a clear evolution of the whole MD field as well as of the usage of the main MD programs. It is worth noting that the number of citations is underestimated, as many publications employing MD simulation do not cite the MD program in the main text, cite other manuscripts, or do not cite any software. However, this problem affects all programs in a similar manner. Also, many other factors might be influencing the number of citations of the MD programs, e.g., AMBER and CHARMM, having a force field with a similar name, might have “wrong” citations that were intended for the force field. We believe that the number of these and other “wrong” citations is not significantly influencing the plot. Data obtained in February 8, 2016.