Molecular simulation analysis and manipulation
Wordom is a (simple) command line utility conceived to spare the user some time in manipulating and converting dcd, xtc, pdb, crd and xyz files. Wordom is also a versatile program for a broad range of molecular structure and dynamics analysis. As a plus, it's easy to use in shell scripts. Due to its simplicity, it is very easy and straightforward to add your own analysis module. Basically, most of what you have to do is write the algorithm - the data are made available by the existing wordom i/o modules.
The Wordom project was conceived and started in the Caflisch Lab at the University of Zurich (CH), Biochemistry dept., and is now maintained and developed mainly in the Fanelli Lab at the University of Modena and Reggio Emilia (IT), Chemistry dept, with contributors from other universities (see developers)
Wordom is free software under the GPL license.
If you use wordom in your work please acknowledge it using the relevant reference(s):
M. Seeber, M. Cecchini, F. Rao, G. Settanni and A. Caflisch; Wordom: a program for efficient analysis of molecular dynamics simulations; Bioinformatics, 2007, 23(19):2625-2627
M. Seeber, A. Felline, F. Raimondi, S. Muff, Ran Friedman, F. Rao, A. Caflisch and F. Fanelli; Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces; J. Comp. Chem., 2011, 6(32):1183-1194; doi:10.1002/jcc.21688
along with any paper which might be relevant to the module/algorithm that you are using (see documentation)
2011/01/25 - version 0.22 (release candidate 2) is OUT!
Old - version 0.22 (release candidate 1) is OUT!
Old - we are actively working at fixing version 0.22 (feature freezed), if you have bugs to point out do it now!
Old - the website has moved to the sourceforge system, with a new doc & tutorials wiki (sf-based, too) and misc stuff