[gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

[Wenjuan Jiang]

Hello  Stéphane,

I happened to use densmap and xpm these days for my ion channel.

Here is an example that you can play with for your system.

gmx densmap -f md.xtc -s md.tpr -n index.ndx -aver z -bin 0.05 -dmin 0
-dmax 20 -unit nm-2 -o md.xpm
( later choose the group you are interested in)

-aver z means we want to get top view, that is going to show your dense map
in xy plane.
-bin width, you can play with it to get best view.  more options, you can
check with densmap -h

gmx xmp2ps -f md.xpm -o md.eps -rainbow blue

eps file can be opened either by eps viewer or photoshop.

Thanks,
Best
Wenjuan


On Tue, Oct 23, 2018 at 7:49 AM ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Dear all,
>
> I would like to obtain a 2D density map plot as for instance Fig. 4 in the
> following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein
> inserted in a surfactant micelle with gmx densmap and xpm2ps .  I have few
> questions
>
> - Have any of you ever done this type of plot? If yes, how?
> - What parameters for densmap and/or xpm2ps did you use?
> - How did you combine the protein and surfactant xpm files into a single
> one to obtain the same plot as Fig. 4
>
> Thanks in advance for your help
>
> Stéphane
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-- 
Best regards

Wenjuan Jiang