NAMD on PARADOX, input preparation, job submission and monitoring, Belgrade, Serbia
Monday, 28 November 2011 -
13:55
Monday, 28 November 2011
13:55
Opening and overview
-
Branko Drakulic
(
Department of Chemistry-IChTM
)
Opening and overview
Branko Drakulic
(
Department of Chemistry-IChTM
)
13:55 - 14:00
Room: 524
14:00
Input files structure, and preparation of files
-
Branko Drakulic
(
Department of Chemistry-IChTM, University of Belgrade
)
Input files structure, and preparation of files
Branko Drakulic
(
Department of Chemistry-IChTM, University of Belgrade
)
14:00 - 16:00
Room: 524
- 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
16:00
Break
Break
16:00 - 16:05
Room: 524
16:05
Job submission, monitoring and upload of results
-
Branko Drakulic
(
Department of Chemistry-IChTM, University of Belgrade
)
Job submission, monitoring and upload of results
Branko Drakulic
(
Department of Chemistry-IChTM, University of Belgrade
)
16:05 - 17:00
Room: 524
- 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