1. Case, D.A., Babin, V., Berryman, J.T., Betz, R.M., Cai, Q., Cerutti, D.S., Cheatham III, T.E., Darden, T.A., Duke, R.E., Gohlke, H., Goetz, A.W., Gusarov, S. Homeyer, N., Janowski, P., Kaus, J., Kolossváry, I., Kovalenko, A., Lee, T.S., LeGrand, S., Lucko, T., Luo, R., Madej, B., Merz, K.M., Paesani, F., Roe, D.R., Roitberg, A., Sagui, C., Salomon-Ferrer, R., Seabra, G., Simmerling, C.L., Smith, W., Swails, J., Walker, R.C., Wang, J., Wolf, R.M., Wu, X., Kollmann, P.A.: AMBER 14. http://ambermd.org . University of California, San Francisco (2014)
2. Brooks, B.R., Brooks III, C.L., Mackerell, A.D., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Caflisch, S.B.A., Caves, L., Cui, Q., Dinner, A.R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R.W., Post, C.B., Pu, J.Z., Schaefer, M., Tidor, B., Venable, R.M., Woodcock, H.L., Wu, X., Yang, W., York, D.M., Karplus, M.: Charmm: the biomolecular simulation program. J. Comp. Chem. 30, 1545–1615 (2009)
3. Hess, B., van der Spoel, D., Lindahl, E.: Gromacs user manual 4.5.4. http://www.gromacs.org/Documentation/Manual/manual-4.5.4.pdf (2010)
4. Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117, 1–19 (1995)
5. Gil, Y., Deelman, E., Ellisman, M., Fahringer, T., Fox, G., Gannon, D., Goble, C., Livny, M., Moreau, L., Myers, J.: Examining the challenges of scientific workflows. Computer 40, 24–32 (2007)