tutorial-1.xml
997f7a8845a2lammm-master-deprecated

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