eucb: A C++ program for trajectory analysis
Introduction
eucb is a free C++ program for analysis of molecular dynamics trajectories in .dcd format (CHARMM/XPLOR/NAMD).
Availability
To obtain the source code, please follow this link (Right click, Save as). You can also get the code with the test files (.psf .pdb .dcd) from this link, or download the test files separately (see below). The file is a tar ball (gzipped), it should compile finely with gcc on a Linux machine. The code does not depend on external libraries, so it can be compiled elsewhere as well.
UNIX/Linux Installation
Unpack the gzipped tar ball file and run the make command:
cd download_path gzip -d eucb.tar.gz tar xvf eucb.tar cd eucb make
eucb executable is placed under the bin directory. Copy this executable to your PATH.
The source code is released under LGPL v3 license.
For questions, suggestions, etc, please e-mail to the authors.
Tutorials and examples
To see online tutorials and examples, please follow this Eucb-wiki. There is also a quick guide in pdf format.
You can download sample MD files (protein+water+ion box) to run the examples:
- complex.psf, PSF file (5.0 MB)
- complex.pdb, PDB file (3.7 MB )
- complex.dcd, DCD file (57 MB, 100 frames)
Or use smaller files without solvent:
- protein.psf, PSF file (269 KB)
- protein.pdb, PDB file (222 KB )
- protein.dcd, DCD file (3.3 MB, 100 frames)
Details about the simulation of C8alpha/C8gamma complex of the sample files can be found from this paper. A local copy is here.
New ideas
We implement new analysis options and incorporate new algorithms as time allows. If you have an interesting point and you want to see eucb to calculate this, please feel free to contact us.
Publication
There is a paper about eucb software:
I.G. Tsoulos and A. Stavrakoudis (2011)
Eucb: A C++ program for molecular dynamics trajectory analysis
Comput Phys Commun, 182:834-841
You may use it to cite the software (if you need so), but you are not required to do so!
Authors
Ioannis G. Tsoulos (itsoulos _at gmail com)
Athanassios Stavrakoudis (astavrak _at uoi gr)
Last Modified
Friday, 6-Aug-2010