Page History

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• Heat_Restart_File: 02_Heat.rst
• Parameter_Topology_File: prmtop
• Production_Control_File: 03_Prod.in

Output Files

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• AMBER_Execution_Summary: 03_Prod.info

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• AMBER_Trajectory_file: 03_Prod.mdcrd

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• AMBER_Execution_log: 03_Prod.out

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• AMBER_Restart_file: 03_Prod.rst
• Amber.oJobID (nothing interesting)

GROMACS

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16

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• Friction_Simulation_Input: in.friction

Output Files

• LAMMPS_Simulation_

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• Log: log.lammps
• LAMMPS.oJobID

ESPRESSO

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16

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Download from https://iu.box.com/espresso

• AlAI_Pseudopotential_File: Al.sample.in
• AlAI_Primitive_Cell: Al.pz-vbc.UPF

• Output Files

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• ESPRESSO_Execution_Log: Al.sample.out

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• ESPRESSO_WFC_Binary_file: Al_exc3.save/ (directory)
• Al_exc3.wfc1
• Al_exc3.wfc2
• Al_exc3.wfc3
• Al_exc3.wfc4 ESPRESSO.oJobID (nothing)

NWCHEM

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16

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• Water_Molecule_Input: water.nw

Output Files

• NWChem_Execution_Log: nwchem_water.out

h2o_freq.b

h2o_freq.drv.hess

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• RNA_Seq_Left_Input: reads.left.fq
• RNA_Seq_Right_Input: reads.right.fq

Output Files

• Trinity_Execution_Log: Trinity - Everything under the specified Output directory
• Trinity_FASTA_File: Trinity.fasta (most interesting maybe)
• Trinity.oJobID

Example Output Directory Contents

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