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Showing 2 open source projects for "coordinates"
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1
ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
...The developed tools include: 1) generator of molecule-water complexes with graphical user interface (GUI), 2) semi-automatic frequency analysis using symbolic potential energy distribution matrix and comparison of optimized internal coordinates, 3) GUI for charge fitting with three modes: manual, Monte-Carlo sampling or brute force, and 4) GUI for dihedral terms fitting. The usage of these tools decreases the labor effort, lowers manual input errors and reduces the time needed for accurate MM parameterization efforts. -
2
md-utils
Utilities to analyze molecular dynamics data
md-utils is a set of command line tools written in C designed to perform certain operations and analysis on the molecular dynamics data. The supported operations involve trajectory coordinate transformation to the COM system, Cartesian coordinate transformation to selected internal coordinates and to projected normal mode coordinates, trajectory merging, selecting subsets of trajectory frames, selecting subsets of atoms, permuting atoms, etc. Analysis tools involve 1D, 2D and 3D data binning (histograms), volumetric data handling, etc. A small library, libmd, is an abstraction layer that serves data exchange among different tools.
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