Embedded Files
AmberTools:
D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D. Cruz eiro, N. Forouzesh, T.J. Giese, A.W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M.C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Manathunga, M.R. Machado, H.M. Nguyen, K.A. O’Hearn, A.V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T.E. Cheatham III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan*, and K.M. Merz,* Jr. AmberTools. J. Chem. Inf. Model. 63, 6183-6191 (2023).
Amber:
D.A. Case, D.S. Cerutti, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, M. Ghazimirsaeed, G.M. Giambasu, T.J. Giese, A.W. Götz, J.A. Harris, K. Kasavajhala, T. Lee, Z. Li, C. Lin, J. Liu, Y. Miao, R. Salomon-Ferrrer, J. Shen, R. Snyder, J. Swails, R.C. Walker, J. Wang, X. Wu, J. Zeng, T.E. Cheatham, III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan*, K.M. Merz*, Jr. Recent Developments in Amber Biomolecular Simulations. J. Chem. Inf. Model. 65, 7835-7843 (2025).
Dr. Nagan's lab makes advanced techniques accessible to the wider computational community. If you have ideas for Amber user support and tutorials, please contact Dr. Nagan. We welcome contributions from the community.
Women Make COMP
Women Make COMP
In collaboration with Prof. Giulia Palermo (UC-Riverside) and Dr. Kira Armacost (GSK), we created a program in ACS COMP for women graduate students and post-doctoral fellows, to find mentors and support from prominent women in the field. This is only a small step to creating a vibrant community for the next generation of women in computational chemistry.
Palermo, G., Armacost, K.A. and Nagan, M.C. " Women Make COMP: Mentoring the Next Generation of Women in Computational Chemistry." J. Chem. Inf. Model. 2019, 59, 10, 4061-4062.
Velay Program
Velay Program
This is a program only available to Stony Brook University undergraduate students and administered through URECA.
Funded by a grant from the Panaphil Foundation.
Dr. Nagan has spent the majority of her career at primarily undergraduate institutions and continues to be committed to involving undergraduate students in research. The Mercury Consortium has been funded by NSF for over 20 years. For articles related to the consortium see:
Shields, G. C., "Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry ( MERCURY )." International Journal of Quantum Chemistry 2020, 120 (20), e26274. DOI: 10.1002/qua.26274
Anderson, K., Arrandondo, S., Ball, A., Bruce, C., Gomez, M., He, K., Hendrickson, H., Madison, L, McDonald, A., Nagan, M., Scott, C., Soto, P., Tomlinson, A., Varner, M., Parish, C., “The impacts of Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) on the Careers of Women in Computational Chemistry.” J. Chem. Inf. Model. 2022 https://doi.org/10.1021/acs.jcim.2c00566
The annual conference is open to all undergraduates conducting computational chemistry research. It is usually held in late July and serves as a friendly, summative experience for undergraduates to give poster presentations. As well, keynote speakers include renowned faculty in computational chemistry, scientists from industry and national labs.
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