27 lines
1.1 KiB
XML
Executable File
27 lines
1.1 KiB
XML
Executable File
<simulation verbosity='high'>
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<initialize nbeads='4'>
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<file mode='pdb' units='angstrom'> our_ref.pdb </file>
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<velocities mode='thermal' units='kelvin'> 25 </velocities>
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</initialize>
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<output prefix='tut1'>
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<properties filename='md' stride='1'> [step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}] </properties>
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<properties filename='force' stride='20'> [atom_f{piconewton}(atom=0;bead=0)] </properties>
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<trajectory filename='pos' stride='100' format='pdb' cell_units='angstrom'> positions{angstrom} </trajectory>
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<checkpoint filename='checkpoint' stride='1000' overwrite='True'/>
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</output>
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<total_steps> 5000 </total_steps>
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<forces>
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<socket mode="inet">
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<address>localhost</address>
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<port> 31415 </port>
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</socket>
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</forces>
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<ensemble mode='nvt'>
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<thermostat mode='pile_g'>
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<tau units='femtosecond'> 25 </tau>
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</thermostat>
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<timestep units='femtosecond'> 1 </timestep>
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<temperature units='kelvin'> 25 </temperature>
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</ensemble>
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</simulation>
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