Creating Simulation Files

A simulation consists of a set of moltemplate (see moltemplate), files which specify LAMMPS simulation settings (forcefield, fixes, molecular structure, etc.), and a set of XYZ files which specify the initial atomic coordinates of the system. The system XYZ file can be most easily created from individual XYZ files with the use of Packmol.

Deploying Simulation

Deploying simulations is done with the create_simulation.py command within the copoly folder of the distribution. An example use of the command would be as follows:

python create_simulation.py -N ${NUMBER_OF_MONOMERS} -fA ${FRACTION_OF_MONOMER_A}\
                             --epsAA ${LIKE_ATTRACTION_AA} --epsBB ${LIKE_ATTRACTION_BB} --epsAB ${UNLIKE_ATTRACTION_AB}\
                              -p ${FINAL_MONOMER_CONVERSION} -f ${DEST_FOLDER} --xyz ${XYZ_FOLDER} --lt ${LT_FOLDER}\
                              --send_to_cluster --slurm

Additional information on all arguments for create_simulation.py can be obtained by running:

python create_simulation.py --help