xtc that only contain coordinate data and no type or topology information. This is especially helpful when using compact binary file formats like. psf file to be used with dump outputs from LAMMPS. In many cases it is much more convenient to use symbolic names for atom types in for visualization and analysis rather then the numbers that LAMMPS uses internally. Topo writelammpsdata data.mysystem molecularīuilding. By default full is assumed, since this is compatible with most types of simulations. To write a LAMMPS data file, you have to know which atom style is going to be used in the input. A typical scenario would be to generate a data file when a software like Packmol is used to generate the starting coorrdinates for systems of groups of identical monomers. This is where the TopoTools plugin aims to help by providing abstract scriptable functions that help to automate the process and thus eliminate the risk of typos or the need for writing a custom program for each new system. The specific format of the data file has several restrictions that make it inconvenient to write it in a text editor from scratch for all by the most trivial systems. In those cases, the individual tools are very well suited for those systems but cannot be easily extended for more general systems. For "bio-systems" the most direct way to get the data file is usually to use the topology building tools of a simulation package like Amber, CHARMM or NAMD and then convert this to a data file with the tools provided with the LAMMPS package. Instead it requires preparing a so-called data file with information about the atoms in the system (atom types, masses, charges, coordinates, bond definitions and types, angles, dihedreals and so on). ![]() The LAMMPS MD simulation package has no internal tools to build systems of bonded atoms or other complex structures.
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