VMD Workshops

Overview

On Feb. 5 and 6 of 1997 the Theoretical Biophysics groupgave two workshops on VMD in the Numerical Lab(NL) of NCSA. The first was on Wednesday and was for people who have used VMD before. The second took place on Thursday and was designed for those who have some experience with Unix but have never used VMD. Nine people attended the advanced workshop and eight participated in the introductory class.

Materials

The schedule and documents for the introductory and advanced workshops are available. The text covered parts of the User's Guide and text distributed on the VMD mailing list as part of a weekly VMDTech series.

The workshop text will be available until the next release of the User's Guide, which will be some time in summer 1997. At that point the hypertext links will no longer point to the correct pages.

The examples required two data files, the PDB structure of bacteriorhopsin and a DCD(21 MB!) animation of the retinal being pulled out. ( Here is a shorter version but still 4 MB.)

Some of the examples require the use of the VMD version 1.2b1 or later. To obtain this binary for SGIs:

  • Install the latest version from ftp.ks.uiuc.edu/pub/mdscope/vmd
  • If this is earlier than 1.2b1, download vmd_IRIX5.Z from ftp.ks.uiuc.edu/pub/group/dalke/
  • Uncompress this file and make it executable.
  • Replace your current version of vmd_IRIX5 in $VMDDIR. You may want to move the previous version of vmd_IRIX5 to vmd_IRIX5.bak in case something goes wrong.

Workshop Format

The workshop format was a mix of lecture, demonstration and hands-on practice. The lectures were limited to short explanations of the underlying topics followed by examples to emphasize important aspects. Most of the workshop, between 60-70%, consisted of self-directed learning aided by web-based tutorials. One or two instructors were available at all times to answer questions of work through difficulties.

Facility

We highly recommend that future VMD workshops be presented in a facility similar to the NCSA NL. The NL for has an Infinity Wall, a 12'x9' screen displaying a 2x2 matrix from 4 high resolution SGIs heads. With this we could should how VMD works in one display, the associated text (in a large font for everyone to see) in another, and the overall schedule in a third. Also present were 10 Indigo2s, so each workshop participant had full access his or her machine.

Most of the programs used during the workshop were remote NFS mounted from the Theoretical Biophysics group computers. By doing so we could ensure that all the specialized software we needed was compiled and available. Also, if there had been any problems we didn't have to acquire root privileges on the NCSA machines to reinstall or reconfigure programs.