NAMD on PARADOX, input preparation, job submission and monitoring, Belgrade, Serbia

Name: NAMD on PARADOX, input preparation, job submission and monitoring, Belgrade, Serbia
Start: 2011-11-28T13:55:00+01:00
End: 2011-11-28T17:00:00+01:00
Location: Faculty of Chemistry, University of Belgrade

Monday 28 Nov 2011, 13:55 → 17:00 Europe/Belgrade

524 (Faculty of Chemistry, University of Belgrade)

524

Faculty of Chemistry, University of Belgrade

Studentski Trg 12-16, Belgrade, Serbia

- 13:55 → 14:00
  
  Opening and overview 5m
  
  Speaker: Branko Drakulic (Department of Chemistry-IChTM)
- 14:00 → 16:00
  
  Input files structure, and preparation of files 2h
  
  - Description of PDB file - Description of PSF file - Usage of topology files - Usage of parameter files - Working example 1UBQ (NAMD native tutorial) - Solving of common problems - Preparation of PDB and PSF files in Windows environment using VegaZZ - Preparation of PDB and PSF files using VMD, native psfgen and command line
  
  Speaker: Branko Drakulic (Department of Chemistry-IChTM, University of Belgrade)
- 16:00 → 16:05
  
  Break 5m
- 16:05 → 17:00
  
  Job submission, monitoring and upload of results 55m
  
  - Transfer of prepared files to user home directory - Basic shell commands - Structure of .pbs and executable script - How to do settings needed - Job submission and monitoring - Inspecting results on PARADOX - Uploading results to user workstation
  
  Speaker: Branko Drakulic (Department of Chemistry-IChTM, University of Belgrade)