Software
| GROMACS Version: 5.1.2 (https://manual.gromacs.org/5.1.2/download.html) LGPL v2.1 (H.J.C. Berendsen, D. van der Spoel and R. van Drunen, 1995, "GROMACS: A message-passing parallel molecular dynamics implementation", Comp. Phys. Comm. 91, 43-56, doi: 10.1016/0010-4655(95)00042-E; B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl, 2008, "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation", J. Chem. Theory Comput. 4, pp. 435-447, doi: 10.1021/ct700301q; Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl, 2013, "GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit", Bioinformatics 29, pp. 845-54, doi: 10.1093/bioinformatics/btt055; Szilárd Páll, Mark J. Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl, 2015, "Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS", In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale, 8759, pp. 3-27, doi: 10.1007/978-3-319-15976-8_1;)
PyEmma Version: 2.5.7 (https://github.com/markovmodel/PyEMMA/tree/v2.5.7) LGPL v3.0 (Martin K. Scherer, Benjamin Trendelkamp-Schroer, Fabian Paul, Guillermo Pérez-Hernández, Moritz Hoffmann, Nuria Plattner, Christoph Wehmeyer, Jan-Hendrik Prinz, and Frank Noé, 2015, "PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models", Journal of Chemical Theory and Computation, 11 (11), 5525-5542, doi: 10.1021/acs.jctc.5b00743)
EncoderMap Version: 0.0.11 (https://pypi.org/project/encodermap/0.0.11/) LGPL v3.0 (Lemke, Tobias, and Christine Peter, 2019, "EncoderMap: Dimensionality Reduction and Generation of Molecule Conformations", Journal of chemical theory and computation, 15.2, 1209-1215, doi: 10.1021/acs.jctc.8b00975)
MDTraj Version: 1.9.3 (https://pypi.org/project/mdtraj/1.9.3/) LGPL v2.1+ (McGibbon, R.T., Beauchamp, K.A., Harrigan, M.P., Klein, C., Swails, J.M., Hernández, C.X., Schwantes, C.R., Wang, L.-P., Lane, T.J., and Pande, V.S., 2015, "MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories", Biophysical Journal 109, 1528-1532, doi: 10.1016/j.bpj.2015.08.015) |