# PREREQUISITES: # # You must use moltemplate.sh to create 3 files: # system.data system.in.init system.in.settings # (Follow the instructions in README_setup.sh, # or run the file as a script using ./README_setup.sh) # ------------------------------- Initialization Section -------------------- include "system.in.init" # ------------------------------- Atom Definition Section ------------------- read_data "system.data" # OPLSAA atom charges are stored in a separate file. # Load that file now: include "system.in.charges" # ------------------------------- Settings Section -------------------------- include "system.in.settings" # ------------------------------- Run Section ------------------------------- # -- minimization protocol -- minimize 1.0e-4 1.0e-6 100000 400000 # -- simulation protocol -- timestep 1.0 print "---------------------------------------------------------------------------" print "First, use Langevin dynamics to randomize the initial shape of the molecules" print "(This is not really necessary, but it seems to speed up equilibration.)" print "---------------------------------------------------------------------------" fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr run 2000 unfix fxlan unfix fxnph print "---------------------------------------------------------------------------" print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" print "---------------------------------------------------------------------------" dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz # temperature: 300 K, pressure: 50 barr fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0 thermo 100 #thermo_modify flush yes run 100000 write_data system_after_npt.data