MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.. MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the. Description. gmx sasa computes solvent accessible surface areas. See Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284 for the algorithm used. With -q, the Connolly surface can be generated as well in a . pdb file where the nodes are represented as atoms and the edges connecting the nearest nodes as. gmx_MMPBSA input file contains all.

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