![]() more powerful and easy to use script commands that make combine multiple low lever commands in a way to solve common tasks conveniently and efficiently.įinally topotools also contains some utilities and applications for more complex operations like combining multiple molecules (=different files) or multiple selections into one new molecule, or building larger systems by replicating a given unitcell. ![]() The topotools packages is supposed to provide a middleware, i.e. The underlying Tcl script API in VMD itself had been designed to be minimalistic, since most operations are not computationally demanding and could be programmed with scripting. Of course write support is also possible. This is especially useful for file formats, where additional input from the user is required, for example reading LAMMPS format "data" (=topology) files, where the "style" of the Atoms section cannot be deduced from the data. In combination with the new command mol new atoms it is now also possible to do many operations directly that previously required writing and manipulating temporary files and reading them back into VMD, or even write complete molecule or simulation data readers in Tcl script. The focus lies hereby on being able to perform many operations manually or scripted and thus being less focused on and optimized for biomolecules like psfgen. This now allows to do a large variety of modifications to topology data or even building topologies from scratch. ![]() not only bonds, but also angle, dihedral, and improper definitions as well as their force field type labels (if available). For us it is always helpful to hear how your existing workflows look like and how you would imagine them to be with the help of OVITO.Starting with VMD version 1.8.7 it is now possible to store the complete topology information, i.e. In the meantime, I can only invite you to express your needs and requirements and let us know what kind of features you wish OVITO to provide in the future. However, I hope we can use the next year to acquire the necessary knowledge and build a team that is able to expand OVITO further in this direction. At the moment, developing such a solution is out of reach for us, because our team does not have the required expertise in that area. The decision will depend on user demand, the availability of existing solutions (we don't want to reinvent the wheel), and the resources we have available as a business.įorce field assignment is a complex task (as far as I can tell as a non-expert), which is also the reason why users wish to have a highly automatized solution. ![]() Force field assignment could be one of them. In the long run, however, we may also consider working on new program features that help building models and setting up simulations. Our short- and mid-term roadmaps (<=1 year) for developing OVITO are focused on further strengthening and extending the viz and analysis capabilities of OVITO. ![]() Its current focus is on visualizing outputs from simulations and providing the tools to analyze them. Quote from Alexander Stukowski on September 22, 2020, 1:16 pmĪs Constanze already mentioned above, OVITO does not have the capability to assign a force field to molecular structures or -more general- to build/construct models and set up simulations. ![]()
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