[gmx-users] how to get a solvent density map using volumeslice in VMD

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Feb 13 18:09:16 CET 2009

Hi Jinyao,

your question is not very well defined. It is considerably easier for  
me if you tell me exactly what you tried to get this to work, which I  
imagine was more than simply running g_spacial once and selecting the  
volume_slice representation in vmd. That said,

1. Can you view it as an isosurface? That is a simpler representation  
to get working and so is a valuable test.

2. Did you try pushing the bar that moves the slicing plane up and down?
2b. Did you try changing the axis and then repeating #2, above?

3. Open the "colors" dialog and go to color scales. When you see the  
volume slice as entirely one color, does that color correspond to full  
strength or no signal?

4. With the color scale mentioned above, try changing the offset and  
magnitude of the gradient and see if that has any effect.

5. What options did you use when you ran g_spatial?


Message: 1
Date: Fri, 13 Feb 2009 16:43:14 +0800
From: "Jinyao Wang" <wangjy at ciac.jl.cn>
Subject: [gmx-users] how to get a solvent density map using
         volumeslice in        VMD
To: "gmx-users" <gmx-users at gromacs.org>
Message-ID: <434514306.04904 at eyou.net>
Content-Type: text/plain;        charset="gb2312"

Hi gmx-users,
I want to get a solvent density map like that in the link  
So I use g_spatial to calculate the spatial distribution function and  
get a *.cube file.
I load the *.cube file into VMD and view it as an volumeslice but no  
anything is displayed.
how can I get the solvent density map? If you have some  
experience,please give me some suggestion.

More information about the gromacs.org_gmx-users mailing list