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Viewing changes to tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/run.in.npt

  • 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_OPLSAA/waterSPCE+methane/run.in.npt
 
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# PREREQUISITES:
 
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#
 
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#     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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#
 
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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_data       "system.data"
 
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# ------------------------------- Settings Section --------------------------
 
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include         "system.in.settings"
 
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include         "system.in.charges"
 
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# ------------------------------- Run Section -------------------------------
 
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# -- minimization protocol --
 
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# Note: The minimization step is not necessary in this example.  However
 
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#       in general, it's always a good idea to minimize the system beforehand.
 
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#       (The "fShakeSPCE" fix was defined in system.in.settings. 
 
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#        It is incompatible with "minimize", so we disable it first.)
 
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unfix         fShakeSPCE
 
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thermo        50
 
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minimize 1.0e-4 1.0e-6 100000 400000
 
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# Now read "system.in.settings" in order to enable fShakeSPCE again:
 
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include       system.in.settings
 
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# Optional: write the coordinates after minimization
 
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write_data   system_after_min.data
 
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# -- simulation protocol --
 
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timestep        1.0
 
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dump            1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
 
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fix             fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
 
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thermo          100
 
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run             2000000
 
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write_data   system_after_npt.data