[gmx-users] -fitall option problems

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 24 12:05:47 CET 2012

Víctor wrote:
> 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. 

The -fitall option is set to 'yes' by default, so invoking it explicitly makes 
no difference.

> Furthermore, the rmsd.xpm file represents a non-symetric matrix, which 
> is not what I expected... Anyone has a clue of what's happening?

I can't explain this.  Perhaps someone else can offer insight.


> Thanks in advance,
> Víctor
> -- 
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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