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Viewing changes to tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/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/waterSPCE+Na+Cl/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, or run it using ./README_sh.)
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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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# ------------------------------- 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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# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize".
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unfix         fShakeSPCE
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minimize 1.0e-3 1.0e-5 100000 400000
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# Now read "system.in.settings" in order to redefine fShakeSPCE again:
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include       system.in.settings
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# -- simulation protocol --
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timestep        1.0
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dump            1 all custom 200 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             10000
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# Now that the system's temperature has become more equilibrated,
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# we can increase the timestep:
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timestep        2.0
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run             50000
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write_data   system_after_npt.data