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Viewing changes to tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt

  • 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/moltemplate_files/system.lt
 
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import "spce.lt"     # <- defines the "SPCE" (water) molecule type.
 
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import "methane.lt"  # <- defines the "Methane" molecule type (uses OPLSAA)
 
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# Periodic boundary conditions:
 
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write_once("Data Boundary") {
 
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   0.0  41.50  xlo xhi
 
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   0.0  41.50  ylo yhi
 
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   0.0  41.50  zlo zhi
 
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}
 
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# The next command generates a (rather dense) cubic lattice with
 
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# spacing 3.45 Angstroms. (The pressure must be equilibrated later.)
 
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waters = new SPCE [12].move(0.00, 0.00, 3.45) 
 
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                  [12].move(0.00, 3.45, 0.00) 
 
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                  [12].move(3.45, 0.00, 0.00)
 
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# Now add methane molecules:
 
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methanes = new Methane [4].move(0, 0, 10.35)
 
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                       [4].move(0, 10.35, 0)
 
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                       [4].move(10.35, 0, 0)
 
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# Move the methane molecules slightly to reduce overlap with the water
 
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methanes[*][*][*].move(1.725, 1.725, 1.725)
 
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