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Viewing changes to tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.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/nanotube+water/moltemplate_files/water_box.lt
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import "spce.lt"
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# --------------- water ------------------
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# Create a rhombohedral box of water. (A rectangular box works also.)
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wat  =  new SPCE  [9].move(3.5526287,    0,      0 )
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                  [9].move(1.77631435, 3.3133,   0 )
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                  [6].move(   0,         0,    3.45)
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# Optional: Center the water box at the origin. (Not really necessary.)
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wat[*][*][*].move(-23.9802437, -14.90985, 11.47)
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# --------------- Note: -----------------
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# The spacing between water molecules does not matter much as long as it is
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# reasonable. (I adjusted the spacing try to insure that the waters are spread 
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# uniformly throughout the box.  We do not want bubles to form if there are 
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# gaps near the XY periodic boundaries.)  We will have to equilibrate it later.
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