3
# You must use moltemplate.sh to create 3 files:
4
# system.data system.in.init system.in.settings
5
# (Follow the instructions in README_setup.sh,
6
# or run the file as a script using ./README_setup.sh)
8
# ------------------------------- Initialization Section --------------------
10
include "system.in.init"
12
# ------------------------------- Atom Definition Section -------------------
14
read_data "system.data"
16
# ------------------------------- Settings Section --------------------------
18
include "system.in.settings"
19
include "system.in.charges"
22
# ------------------------------- Run Section -------------------------------
25
# -- minimization protocol --
27
# Note: The minimization step is not necessary in this example. However
28
# in general, it's always a good idea to minimize the system beforehand.
29
# (The "fShakeSPCE" fix was defined in system.in.settings.
30
# It is incompatible with "minimize", so we disable it first.)
33
minimize 1.0e-4 1.0e-6 100000 400000
35
# Now read "system.in.settings" in order to enable fShakeSPCE again:
36
#include system.in.settings
38
# Optional: write the coordinates after minimization
39
write_data system_after_min.data
42
# -- simulation protocol --
46
dump 1 all custom 2500 traj_npt.lammpstrj id mol type x y z ix iy iz
47
fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
52
write_data system_after_npt.data