Egon and everyone, Angel used the GROMACS utility "editconf" to convert a GROMACS file to a Jmol-readable file. Heres another way:
Check out the trjconv utility within your installation of GROMACS: www.gromacs.org/documentation/reference_3.3/online/trjconv.html trjconv will read a GROMACS trajectory file (.xtc or .trr) and output a .pdb file, e.g.: trjconv f trajectory.xtc s topol.tpr o pdbtrajectory.pdb -f = input trajectory -s = structure file (used for grompp) o = output file The structure file allows trjconv to parse the trajectory. So: 1. use trjconv to generate a .pdb file. 2. load the .pdb file into Jmol Animate! ?This is the really cool part. Two more comments: Because trajectory files tend to be large, you have to be aware of the memory limitations of Jmol. Recently, Jmols handling of memory errors has significantly improved. (Thanks, Bob!) The Jmol wiki shows how to offer the Jmol application more memory: http://wiki.jmol.org:81/index.php/Jmol_Application Note, of course, that trjconv is a trajectory editor. Options include skipping frames, ignoring solvent, ignoring dull parts of an otherwise interesting molecule, centering a molecule of interest, etc. In principle, these kinds of things could be duplicated in a Jmol command...but you'd be duplicating the trjconv utility at the expense of having Jmol work with some very large files. In principle, it may be possible to set up a GROMACS simulation to save a .pdb trajectory with only the parts of the trajectory that you want to feed to Jmol, but the compromise between a true analysis of a trajectory vs a visualization of a trajectory may be too great. And the trjconv editor works great. Matt -----Original Message----- From: Angel Herraez [mailto:angel.herr...@uah.es] Sent: Tue 2/10/2009 8:34 AM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Jmol and GROMACS? Egon, this page of mine http://biomodel.uah.es/en/water/p3.htm was built from Gromacs data of a molecular dynamics simulation. Since Jmol did not read the gro file, I converted the data to pdb format (see details at the bottom of the page). We discussed about providing Jmol support for gro files, but I think it was not done -- if I remember correctly, Bob needed good sample files for proteins, which I don't have. See the discussion at http://sourceforge.net/tracker/?func=detail&atid=379136&aid=1876675&gr oup_id=23629 ------------------------------------------------------------------------------ Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
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