![]() Resets per atom data through selected heuristics. Returns the list of unique atom types names. Returns the number of atom types as determined from the type property. bondorder bond order parameter (default: 1) numatoms All command lines start with the topo keyword and then take a subcommand name to determine the actual functionality that is requested. This is modeled after the example of the internal mol or molinfo commands, or the pbc command from the PBCTools package to provide a somewhat consistent interface to the functionality. This is the middleware part of the package that provides abstract operations on top of the low-level API. This documentation describes the version of the topotools plugin that is displayed in the title. ![]() This page also links to a set of tutorial examples that demonstrate in moreĭetail, how the commands in the plugin can be used to build topologyĭata files for different kinds of MD simulation packages. Updates and bug fixes for topotools between VMD releases Larger systems by replicating a given unitcell. (=different files) or multiple selections into one new molecule, or building Multiple low lever commands in a way to solve common tasks convenientlyįinally topotools also contains some utilities andĪpplications for more complex operations like combining multiple molecules more powerful and easy to use script commands that make combine Topotools packages is supposed to provide a middleware, The underlying Tcl script API in VMD itself had beenĭesigned to be minimalistic, since most operations are notĬomputationally demanding and could be programmed with scripting. Of course write support is also possible. User is required, for example reading LAMMPS format "data" (=topology)įiles, where the "style" of the Atoms section cannot be deducedįrom the data. Is especially useful for file formats, where additional input from the Write complete molecule or simulation data readers in Tcl script. Possible to do many operations directly that previously required writingĪnd manipulating temporary files and reading them back into VMD, or even Thus being less focused on and optimized for biomolecules like Hereby on being able to perform many operations manually or scripted and Topology data or even building topologies from scratch. ![]() This now allows to do a large variety of modifications to Improper definitions as well as their force field type labels (ifĪvailable). not only bonds, but also angle, dihedral, and Starting with VMD version 1.8.7 it is now possible to store the complete
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