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

[Wenjuan Jiang]

Hi  Stéphane

I am interested in the lipid density around the protein, so I only choose
the lipid bilayer to plot 2D density map.

Regarding the coordinates, I need to remove the pbc box effect by 'pbc mol'
of trajconv function so that the protein will be complete, or in Amber,
cpptraj with autoimage function, and this will not affect the function of
densmap and xpm2ps. The 2D without pbc will look like pieces of protein. In
this sense, I think yes, you need to do preprocessing before 2D densemap

Best,
Wenjuan

On Wed, Oct 24, 2018 at 1:21 AM ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> 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
>
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-- 
Best regards

Wenjuan Jiang