[gmx-users] solvent spatial distribution

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Dec 28 05:39:06 CET 2008

I agree with Mark, your question is not well formed. Perhaps what you  
are interested in can be obtained in the following way.

1. run g_spatial and load the grid.cube file in to vmd.
2. select the "volume slice" representation with the x/y/or z view as  
you desire
3. Find a way to superimpose a circle of radius 0.43 nm
    You can do this in VMD with "draw circle {x,y,x} radius r" (or  
something like that) or you can use gimp/photoshop provided you give  
yourself the appropriate reference points, which could be added by  
modifying the grid.cube file to include extra "atoms" that can guide  
you in the appropriate plane. I often use this second technique in  
which I render 2 images from VMD, one with the reference and one  
without. I then load them into gimp as separate layers of the same  
image with the reference one on top. I then draw a circle (or  
whatever) on a third transparent top layer and then delete the layer  
that had the reference. This way, what you get is a perfectly modified  
figure that no longer has your not-very-pretty reference dots.

Note, if none of the 3 available volume slice planes works just as you  
would like it, then first trjconv -princ or trjconv -rotate your  
trajectory prior to g_spatial (trjconv -center, trjconv -princ/rotate,  
generate a tpr, trjconv fit -s new.tpr, g_spatial);

If you want more help then you need to paint a picture of exactly what  
you want to do.


Jinyao Wang wrote:
> gmx-users=A3=AC
> =20
> I have computed the rdf between a atom of solvent and a atom of solute=20
> and get rmin=3D0.43nm.I have also known the g_spatial can compute=20
> the solvent spatial distribution around a atom of solute. I could get=20
> a 3D solvent spatial distribution plot if I load the grid.cube into VMD=
> But if I want to get a 3D solvent spatial distribution plot within r<=3D=
> I don't know how to do it. Any suggestion will be appreciated.

I'm not sure I understand your problem, but if you've computed an RDF
with a GROMACS tool, then you have it in an .xvg file. You can visualize
that immediately with GRACE, or other tools. See


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