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Viewing changes to tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/run.in.nvt

  • 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/force_field_AMBER/ethylene+benzene/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, 
 
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#       or run the file as a script using ./README_setup.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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# ------------------------------- 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_data   system_after_nvt.data