![]() VMD 1.9.3 contains many features for generating high quality renderings of molecular graphics and for creation of movies of both static structures and molecular dynamics simulation trajectories.The collective variables module implemented in VMD (and shared with NAMD and LAMMPS) incorporates many new features and improvements, including: histogram calculation on ensembles of variables, with optional weights probability distribution restraints analysis newly contributed variable types "dipoleAngle" (Alejandro Bernardin), "groupCoordNum" (Alan Grossfield) scripting command "cvcflags" to optimize performance of complex colvars and improved error handling in user input and scripting.Both the MDFF GUI and command line plugins now use CHARMM36 as the default parameter set. ![]() The cispeptide, chirality, and the new TorsionPlot, and QwikMD plugins now connect to the MDFF GUI to simplify finding and fixing errors or setting up your structure for MDFF. The MDFF graphical user interface (GUI) in the Modeling section of the VMD Extensions menu has been updated to reflect the use of multiple maps in addition to many other usability improvements. The MDFF setup plugin now supports the use of multiple density maps in a single MDFF simulation.
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