Software contributions to download
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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
README.rescue). The actual files are
README.rescue. O. Beckstein has added large file
support for linux.
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
The script is available from the Gromacs Software Contributions (direct link
gmx_rescue.tgz) or from this server (gmx_rescue.tgz).
VRPN Library v06.03 with Phantom support for SGI and
This version of the VRPN (Virtual Reality Peripheral
Network) library is an adaptation in order for the Phantom
server to run on SGIs using GHOST 3.1 (nowadays support for
Phantom under SGI is stopped). I haven't tested whether the
changes that I have contributed still work for more recent
versions of the library.
Making the necessary changes in the library wouldn't have been
possible without the invaluable help of David Marshburn,
Adam Seeger, John Stone and Russell M. Taylor II.
The tarball of the modified version can be downloaded from
this server (VRPN v06.03 tarball).
Opera bookmark to XML converters
There are two perl scripts to convert and manipulate Opera
bookmark files. They are an extension of the op2xbel script
originally written in Python by Lars Marius Garshol and
rewritten in perl by Briac Pilpréby. On one hand the script
was modified to extract a complete subfolder of a huge opera
bookmark file (op2self). On the other hand, one can export
into a docbook conforming XML document instead of Opera
adr to xbel conversion (op2docbook). The docbook XML source
can then eg be included as a chapter or so in a docbook
The scripts are available from this server (op2self,