I've having some problems with use of the option '-fitall'.<div><br></div><div>The command I'm using is:</div><div>g_rms -hidden -fitall -s ../topol_amber.tpr -f ../amber99sb_skip10.xtc -f2 ../amber99sb_skip10.xtc -m rmsd.xpm<br>
<br>But a diff with the rmsd.xpm file I got without using '-fitall' reveals that the files are identical. </div><div><br></div><div>Furthermore, the rmsd.xpm file represents a non-symetric matrix, which is not what I expected... Anyone has a clue of what's happening?</div>
<div><br></div><div>Thanks in advance,</div><div>Víctor</div><div><br><div class="gmail_quote">On Mon, Jan 23, 2012 at 5:12 PM, Víctor <span dir="ltr"><<a href="mailto:victor.gil.sepulveda@gmail.com">victor.gil.sepulveda@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Yes, thanks. My first impulse was to do a python script to do the conversion, but Tsjerk Wassenaar's script works neat :)<div>
<div></div><div class="h5"><div><br><div class="gmail_quote">On Mon, Jan 23, 2012 at 5:10 PM, lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com" target="_blank">lina.lastname@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>On Mon, Jan 23, 2012 at 9:56 PM, Víctor <<a href="mailto:victor.gil.sepulveda@gmail.com" target="_blank">victor.gil.sepulveda@gmail.com</a>> wrote:<br>
> Dear all,<br>
><br>
> I've been trying to do a rmsd matrix of two different trajectories by using<br>
> g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms<br>
> uses does something like this:<br>
><br>
> for each frame f1 in traj1:<br>
> for each frame f2 in traj2:<br>
> superimpose f1 , f2<br>
> calculateRMSD f1, f2<br>
><br>
> Or like this (as I've seen in some other rmsd matrix calculation scripts):<br>
><br>
> for each frame f in traj1:<br>
> superimpose f with first frame<br>
><br>
> for each frame f1 in traj1:<br>
> for each frame f2 in traj2:<br>
> calculateRMSD f1, f2<br>
><br>
> I've also been trying to convert the resulting xpm file to a readable file<br>
<br>
</div>BTW, xpm file is readable.<br>
try:<br>
more xpm or other tools your preferred to read.<br>
<div><br>
<br>
> in order to process it using python. Is there any tool to do this kind of<br>
> conversion?(Btw I've been trying to find this kind of tool with not much<br>
> luck). There's enough info on the file to be able to parse it easily, but<br>
> using a 3rd party tested tool would be more convenient.<br>
><br>
> Thanks!<br>
><br>
> --<br>
><br>
> Víctor Gil Sepúlveda<br>
> E. Informatica - FIB - UPC<br>
><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><br>Víctor Gil Sepúlveda<br>E. Informatica - FIB - UPC<br>
</div>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><br>Víctor Gil Sepúlveda<br>E. Informatica - FIB - UPC<br>
</div>