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

[ABEL Stephane]

Hi Wenjuan,

Thank you for response is it useful. I have an additional question, did you plot in the same xpm figure the 2D dens profiles for the protein and the lipids (since I suppose you simulated in a membrane)? 

An additional comment, here 
Since your channel was simulated in a bilayer you used the  xtc generated during the MD without coordinate manipulations (correct ?). In my case, the MP is inserted in a micelle and thus the MP detergent complex can freely rotate move during the MD so I need to reorient the complex according the z axis "before" to use gmx densmap, correct ?

Thanks you 

Stéphane

------------------------------

Message: 5
Date: Tue, 23 Oct 2018 23:31:22 -0700
From: Wenjuan Jiang <sibylaries at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] parameters for plotting 2D density map with
        gmx densmap and xpm2ps
Message-ID:
        <CAJFfpqotdvMwTW5zkQPtYBTPETcr7HqY4ZzhL7j=SPrhAA8trA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hello  St?phane,

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
>
> St?phane
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--
Best regards

Wenjuan Jiang