Branko Drakulic
(Department of Chemistry-IChTM, University of Belgrade)
28/11/2011, 14:00
- 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
Branko Drakulic
(Department of Chemistry-IChTM, University of Belgrade)
28/11/2011, 16:05
- 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
