This directory contains examples for the "moltemplate" molecule builder for LAMMPS. http://www.moltemplate.org
Each directory contains one or more examples.
Each example directory contains the following files and directories:
| File or directory | Explanation |
|---|---|
| images/ | This folder has pictures of the molecules in the system |
| moltemplate_files/ | This folder contains LT files and other auxiliary files |
| README_setup.sh | Instructions for how to use moltemplate (executable) |
| README_visualize.txt | Instructions for viewing in DATA/DUMP files in VMD |
...and one or more LAMMPS input scripts with names like "run.in.min", "run.in.npt", and "run.in.nvt". These input scripts load the files you created with moltemplate which describe the system that you wish to simulate. They also contain a (usually minimal) list of additional LAMMPS commands needed to run the simulation under reasonable conditions (specifying timesteps, integrators, and output file names, for example).
You can run these LAMMPS scripts using
lmp_mpi -i run.in.npt
(The name of your lammps binary, "lmp_mpi" in this example, may vary. Sometimes, these scripts must be run in a certain order. For example it may be necessary to run run.in.min to minimize the system before you can use run.in.npt, and later run.in.nvt. The README_run.sh file in each subdirectory specifies indicates the order. Many of these script files have not been optimized.)