I've having some problems with use of the option '-fitall'. The command I'm using is: g_rms -hidden -fitall -s ../topol_amber.tpr -f ../amber99sb_skip10.xtc -f2 ../amber99sb_skip10.xtc -m rmsd.xpm
But a diff with the rmsd.xpm file I got without using '-fitall' reveals that the files are identical. Furthermore, the rmsd.xpm file represents a non-symetric matrix, which is not what I expected... Anyone has a clue of what's happening? Thanks in advance, Víctor On Mon, Jan 23, 2012 at 5:12 PM, Víctor <victor.gil.sepulv...@gmail.com>wrote: > Yes, thanks. My first impulse was to do a python script to do the > conversion, but Tsjerk Wassenaar's script works neat :) > > On Mon, Jan 23, 2012 at 5:10 PM, lina <lina.lastn...@gmail.com> wrote: > >> On Mon, Jan 23, 2012 at 9:56 PM, Víctor <victor.gil.sepulv...@gmail.com> >> wrote: >> > Dear all, >> > >> > I've been trying to do a rmsd matrix of two different trajectories by >> using >> > g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm >> g_rms >> > uses does something like this: >> > >> > for each frame f1 in traj1: >> > for each frame f2 in traj2: >> > superimpose f1 , f2 >> > calculateRMSD f1, f2 >> > >> > Or like this (as I've seen in some other rmsd matrix calculation >> scripts): >> > >> > for each frame f in traj1: >> > superimpose f with first frame >> > >> > for each frame f1 in traj1: >> > for each frame f2 in traj2: >> > calculateRMSD f1, f2 >> > >> > I've also been trying to convert the resulting xpm file to a readable >> file >> >> BTW, xpm file is readable. >> try: >> more xpm or other tools your preferred to read. >> >> >> > in order to process it using python. Is there any tool to do this kind >> of >> > conversion?(Btw I've been trying to find this kind of tool with not much >> > luck). There's enough info on the file to be able to parse it easily, >> but >> > using a 3rd party tested tool would be more convenient. >> > >> > Thanks! >> > >> > -- >> > >> > Víctor Gil Sepúlveda >> > E. Informatica - FIB - UPC >> > >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > > Víctor Gil Sepúlveda > E. Informatica - FIB - UPC > -- Víctor Gil Sepúlveda E. Informatica - FIB - UPC
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