# Documentation

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The DoSPT code is structured around several input files that serve the purpose of:

• Providing the MD trajectory information, that is atomic positions (and possibly velocities). This info is contained in a trajectory file, that can be supplied in a variety of popular formats (e.g., traj.gro or traj.xyz).
• Defining atomic groups.
• Defining atomic supergroups.
• Providing masses information for the atoms involved in the MD.
• Containing all the input options and other miscellaneous information pertaining your simulation, such as time step, etc. The input file can contain minimal input parameters or it can contain special keywords that allow you to fine tune the simulation parameters, e.g., allow you to switch on pre- and post-processing of trajectory data or to choose between different available implementations of the hard-sphere formalism.

These input files should all be present within the directory where DoSPT is to be executed. Read through the description of each input file to familiarize yourself with the expected format and the scope/effect of the different input parameters accepted by DoSPT.

An optional input file is the topology file. The topology file contains bond and molecule information that allows DoSPT to handle bond breaking and bond formation dynamically (that is, as it happens during the MD run).

DoSPT input files
Required Optional
input, groups, supergroups, masses, traj.*** topology

You can also check out the wishlist, which summarizes wanted and planned functionality to be (hopefully) incorporated to DoSPT.