Page History

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• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16 or 32

Inputs

Download from https://iu.box.com/wrf

• Config_Namelist_File: namelist.input 
• WRF_Boundary_File: wrfbdy_d01
• WRF_Initial_Conditions: wrfinput_d01 

Outputs

AMBER

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• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 416 or 32

Input Files

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

• Heat_Restart_File: 02_Heat.rst
• Parameter_Topology_File: prmtop
• Production_Control_File: 0303_Prod.in
• prmtop

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: 416

Input Files

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

• GROMOS_Coordinate_File: pdb1y6l-EM-vacuum.gro
• Portable_Input_Binary_File: pdb1y6l-EM-vacuum.tpr

Output Files

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• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 416

Input Files

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

• pdb1y6l-EM-vacuum.tprFriction_Simulation_Input: in.friction

Output Files

...

• LAMMPS_Simulation_Log: log.lammps
• LAMMPS.oJobID

ESPRESSO

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 416

Input Files

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: 416

Input Files

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

• Water_Molecule_Input: water.nw

Output Files

• NWChem_Execution_Log: nwchem_water.out

h2o_freq.b

h2o_freq.drv.hess

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• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 416

Input Files

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

• 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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• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 416

Input Files

AD4_parameters.dat: Download from https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/autodock

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• AD4_parameters.dat

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• hsg1.A.map

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• hsg1.C.map

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• hsg1.d.map
• hsg1.e.map

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• hsg1.HD.map

...

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• hsg1.maps.fld
• hsg1.NA.map

...

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• hsg1.N.map
• hsg1.OA.map

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• ind.dpf

...

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• ind.pdbqt

Output Files

ind.dlg Autodock.oJobID (nothing interesting)