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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12769 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-11-24 17:02:36 +00:00
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174
tools/i-pi/examples/tutorial/tutorial-3/our_ref.pdb Executable file
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END

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tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_npt.xml Executable file
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<simulation verbosity='medium'>
<initialize nbeads='16'>
<file mode='chk'> tutorial-3_RESTART </file>
</initialize>
<output prefix='tut3_npt'>
<properties filename='md' stride='1'> [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}, pressure_cv{megapascal}, volume ] </properties>
<trajectory filename='pos' stride='100' format='pdb' cell_units='angstrom'> positions{angstrom} </trajectory>
<checkpoint filename='checkpoint' stride='1000' overwrite='True'/>
</output>
<total_steps> ??? </total_steps>
<forces>
<socket mode="???">
<address>localhost</address>
<port> 31415 </port>
</socket>
</forces>
<ensemble mode='npt'>
<barostat mode='???'>
<thermostat mode='???'>
<tau units='femtosecond'> ??? </tau>
</thermostat>
<tau units='femtosecond'> ??? </tau>
</barostat>
<thermostat mode='???'>
<tau units='femtosecond'> ??? </tau>
</thermostat>
<timestep units='femtosecond'> ??? </timestep>
<temperature units='kelvin'>25</temperature>
<pressure> 0 </pressure>
</ensemble>
</simulation>

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tools/i-pi/examples/tutorial/tutorial-3/tutorial-3_nvt.xml Executable file
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<simulation verbosity='medium'>
<initialize nbeads='16'>
<file mode='pdb'> our_ref.pdb </file>
<velocities mode='thermal' units='kelvin'> ??? </velocities>
</initialize>
<output prefix='tut3_nvt'>
<properties filename='md' stride='1'> [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}, pressure_cv{megapascal} ] </properties>
<trajectory filename='pos' stride='100' format='pdb' cell_units='angstrom'> positions{angstrom} </trajectory>
<checkpoint filename='checkpoint' stride='1000' overwrite='True'/>
</output>
<total_steps> ??? </total_steps>
<forces>
<socket mode="???">
<address>localhost</address>
<port> 31415 </port>
</socket>
</forces>
<ensemble mode='nvt'>
<thermostat mode='???'>
<tau units='femtosecond'> ??? </tau>
</thermostat>
<timestep units='femtosecond'> ??? </timestep>
<temperature units='kelvin'>25</temperature>
</ensemble>
</simulation>