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. VMD 1.9.3 contains several updates for the Molecular Dynamics Flexible Fitting (MDFF) Method.Documentation and screencast tutorials are available on the plugin website. In addition to the major tools described above, ffTK contains several new but smaller features, such as the ability to output the MM relaxed conformational scan used as the baseline in dihedral fitting, and bug fixes.Numerical analysis can also be performed to provide detailed information on how all dihedrals change throughout the scan, helping to identify highly coupled torsions that often complicate parameter fitting. The key function of this tool is to load each optimized structural conformation into VMD and to construct a color plot of the associated potential energy surface (PES) for side-by-side comparison. A new analysis and plotting utility, named Torsion Explorer (accessable from the Scan Torsions tab), is designed specifically to aid in troubleshooting difficult dihedral parameter fits providing visual and numerical analysis of the relaxed QM torsion scans. ffTK can now leverage the output from this resource to automatically prepare the PSF+PDB files required by ffTK, analyze penalty scores associated with each returned parameter, visualize all instances of a given parameter directly within the molecular structure, and write a parameter file that is initialized to the CGenFF values as a starting point for refinement. The CGenFF Program web server performs an analysis of molecular structure and assigns parameters based on analogy to molecules contained with in the standard CGenFF parameter set. A new tool has been added to the BuildPar toolset that processes output from the CGenFF Program webserver to automatically construct all of the structural and parameter input required for entry into the ffTK parameterization workflow, bypassing a common stumbling block in structure preparation.Two new major features have been added to the Force Field Toolkit for the VMD 1.9.3 release. The Force Field Toolkit (ffTK) plugin provides a comprehensive toolset for the development of CHARMM-compatible (e.g., CGenFF) force field parameters, including charges, bonds, angles, and dihedrals.QwikMD incorporates logging of procedures for reproducibility, and to enable simulation workflows and protocols to be shared among users. For more information, the user is redirected to web-pages through links present in the bottom of the information window. Each "info button" generates a window where the user can find fundamental information related to Molecular Dynamics simulations, such as the description of solvent models and protein structure, as well as short explanations of the options available in QwikMD graphical interface and the actions triggered by the buttons. While making it easy for a new user to perform simulations, QwikMD also works as a learning tool with "info buttons" that guide the user and provide the theoretical background underlying the procedures that are followed. Connecting the user-friendly molecular graphics program VMD to the widely adopted MD program NAMD, the new QwikMD plugin guides users to prepare common molecular simulations in just a few minutes, allowing for quickly study of point mutations, partial deletions or even steering experiments.
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