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  • Committer: Package Import Robot
  • Author(s): Anton Gladky
  • Date: 2015-04-29 23:44:49 UTC
  • mfrom: (5.1.3 experimental)
  • Revision ID: package-import@ubuntu.com-20150429234449-mbhy9utku6hp6oq8
Tags: 0~20150313.gitfa668e1-1
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tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/run.in.nvt
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# PREREQUISITES:
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#
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#   1) You must use moltemplate.sh to create 3 files:
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#        system.data  system.in.init  system.in.settings
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#     (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
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#   2) You must equilibrate the system beforehand using "run.in.npt".
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#      This will create the file "system_after_npt.data" which this file reads.
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#      (Note: I have not verified that this equilibration protocol works well.)
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# ------------------------------- Initialization Section --------------------
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include         "system.in.init"
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# ------------------------------- Atom Definition Section -------------------
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# Read the coordinates generated by an earlier NPT simulation
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read_data       "system_after_npt.data"
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# OPLSAA atom charges are stored in a separate file.
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# Load that file now:
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include         "system.in.charges"
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# ------------------------------- Settings Section --------------------------
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include         "system.in.settings"
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# (The "write_restart" and "read_restart" commands were buggy in 2012, 
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#  but they should work also.  I prefer "write_data" and "read_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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# -- simulation protocol --
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timestep        1.0
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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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fix             fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
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thermo          500
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#thermo_modify  flush yes
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run             200000
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write_restart   system_after_nvt.data