This example demonstrates how to build a simulation containing a box of methane gas. (Not a very interesting example.)
The methane molecules in this example use the OPLSAA force-field. This means that the database of force-field parameters in "oplsaa.lt" will be used to generate angles, dihedrals, and impropers. The "moltemplate_files/methane.lt" file contains these lines which refer to OPLSAA:
import "oplsaa.lt"
Methane inherits OPLSAA { ... } # (see "methane.lt")
The number of molecules and simulation box size can be controlled by editing the system.lt file. The simulation contitions can be controlled by editing the run.in.npt file.
More detailed instructions on how to build LAMMPS input files and run a short simulation are provided in other README files.
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To build the files which LAMMPS needs, follow the instructions in: README_setup.sh
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To run LAMMPS with these files, follow these instructions: README_run.sh
(The instructions in "README_remove_irrelevant_info.sh" are optional. (If you notice a problem with this example, please report it.)
In this example, atomic charge for OPLSAA atoms is determined by @atom type (...according to a lookup table located at the beginning of the "oplsaa.lt" file). (Any atomic charges listed in the "Data Atoms" section of your molecules' LT files will be ignored.) These charges can be overridden. See here for instructions explaining how to customize atomic charge.