[gmx-users] g_sham

Justin Lemkul jalemkul at vt.edu
Mon Oct 14 13:56:41 CEST 2013

On 10/14/13 7:54 AM, pratibha kapoor wrote:
> Dear all gromacs users
> I am creating free energy landscape using g_sham but my axis are not
> getting labelled. I have searched the archive and found that using xmin and
> xmax options we can label them.
> I have first created my 2D projection xvg file using
> g_anaeig -f *.xtc -s *.tpr -first 1 -last 2 -2d *.xvg -v *.trr
> and then found  min and max values for both the vectors,
> say for vector1 min:-2.25 and max:1.83
> and for vector2 min:-1.60 and max: 2.22
> and then I have used:
> g_sham -f *.xvg -ls *.xpm -notime -xmin -2.25 -1.60 0 -xmax 1.83 2.22 0
> and then converted *.xpm to *.eps using
> xpm2ps -f *.xpm -o *.eps -rainbow blue
> This way I got eps file with only one axis(x axis) labelled and following
> line appeared:
> Auto tick spacing failed for Y-axis, guessing 1.19375
> I would like to ask is this way of labelling the axis correct? If yes, why
> didn't y axis get labelled and how to solve the problem?

xpm2ps has very limited ability to label axis intelligently.  If your x- and 
y-axes are not easily divisible, then it fails (hence what it tells you above). 
  You have set minima and maxima that are not easily divisible by one another, 
so tick spacing will not work nicely.  Try ±2.5 for your data range in g_sham.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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