mirror of https://github.com/lammps/lammps.git
54 lines
2.0 KiB
Plaintext
54 lines
2.0 KiB
Plaintext
# ------------------------------- Initialization Section --------------------
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include system.in.init
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# ------------------------------- Atom Definition Section -------------------
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# Normally, I would minimize the system and equilibrate the system at constant
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# pressure and temperature beforehand. If you run lammps with "run.in.npt",
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# it will generate a restart file "system_after_npt.rst" with reasonable
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# coordinates at that temperature and pressure. Then we could load it now:
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#
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#read_restart system_after_npt.rst
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#
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# Unfortunately the LAMMPS "read_restart" command has been undependable over
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# the past year (2012), and I feel it is safer to remove it from the examples.
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# Instead, for this example, I just read the raw coordinates generated by
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# moltemplate (and the default volume). (I get fewer questions this way.)
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# However you should never run any liquid simulations at constant volume without
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# pressure equilibration first. Hopefully in the future "read_restart" will
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# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
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read_data system.data
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# ------------------------------- Settings Section --------------------------
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include system.in.settings
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# ------------------------------- Run Section -------------------------------
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timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
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dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
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thermo_style custom step temp pe etotal vol epair ebond eangle
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thermo 1000 # time interval for printing out "thermo" data
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fix fxlan all langevin 300.0 300.0 120 48279
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fix fxnve all nve
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# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
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# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
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# Note: The langevin damping parameter "120" corresponds to
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# the 0.12ps damping time used in Watson et. al JCP 2011.
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#restart 1000000
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run 1000000
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write_restart system_after_nvt.rst
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