Sidebar - a very simple converter script to make VMD read OpenDX exports

This is a simple shell script to convert OpenDX data for use in VMD. It makes VMD read OpenDX exports using the "text follows" format available in OpenDX. The script creates a pseudo-Opendx file on standard output that can be read in as volumetric data by VMD. Input is an opendx file <opendx> exported via the "text follows" option. The "conversion" is extremely simple and could be improved if necessary. The name of the dataset is given as second argument.

The script is available from this server ( - a very simple generator for OpenDX import of maestro sitemaps

This is a shell script that creates an OpenDX .general import filter for direct import of binary .vis files generated by Schroedinger's Maestro program with options like sitemaps. The name of the dataset is given as second argument.

The script is available from this server (

top2psf - convert Gromacs topology files to PSF files usable by VMD

This is a perl script to convert a Gromacs topology file (.TOP/.ITP) or alternatively a PDB file with Connect records in a Charmmm/Xplor psf file using the information about atom types, charges, masses and bonds. Then one can use VMD to visualize pdb+psf and verify whether the bonding topology is ok. It is based on the gmx2mmc script by Graham Smith.

If you try to use the script on a complex system (more than just a protein, maybe some lipids plus water and so on), then you should use the preprocessed topology file, i.e. the one you get from using grompp's -pp option.

The script is available from the VMD Script Library (direct link top2psf) or from this server (top2psf).

gmx_rescue - recover corrupted Gromacs trajectories (xtc files)

This is a utility to rescue partly corrupted XTC files. It works under Linux and is based on earlier files contributed for SGI (see README.rescue). The actual files are called gmx_rescue.c and README.rescue. O. Beckstein has added large file support for linux and does also provide the program on his software page.

This tool came in handy for me because a lot of simulations that I had run on some supercomputer had corrupted XTC files (apparently due to hardware problems or NFS errors). Rescuing them made me (up to now) just loose about 10 frames in 2500, so I think this is still acceptable and avoids re-running the simulations.

The script is available from the Gromacs Software Contributions (direct link gmx_rescue.tgz) or from this server (gmx_rescue.tgz).