This example is a simple simulation of 288 hexadecane molecules in a box at room temperature and atmospheric pressure. Please read the WARNING.TXT file. -------- REQUIREMENTS: --------- This example requires building LAMMPS with the "USER-MISC" package. (because it uses dihedral_style fourier) To do this, type "make yes-user-misc" before compiling LAMMPS. http://lammps.sandia.gov/doc/Section_start.html#start_3 More detailed instructions on how to build LAMMPS input files and run a short simulation are provided in other README files: step 1) to setup the LAMMPS input files, run this file: README_setup.sh step 2) to run LAMMPS, follow the instructions in this file: README_run.sh ------------ NOTE: There are two versions of this example. ---------------- Both examples use the same force-field parameters. 1) In this directory, all of the force-field parameters are listed explicitly in the "alkanes.lt" file (located in the "moltemplate_files" directory). This allows the user to manually control all of the force-field details. 2) However, there is an alternate version of this example in the "../AMBER_force_field_examples" directory. In that version, the force-fields are loaded from a much larger file named "gaff.lt" which contains all of the parameters in the AMBER GAFF force-field database. The "gaff.lt" is similar to the "alkanes.lt" file except that it is larger (because it contains information for nearly all small organic molecules). It is located in a different directory (in the "common" directory). Relying on "gaff.lt" frees the user from the drudgery of manually specifying all of these force-field details for every molecule. (However, the user must be careful to choose @atom-type names which match AMBER GAFF conventions, such as "c3" and "h1", in this example.)