[gmx-users] Re: Chris

Jinyao Wang wangjy at ciac.jl.cn
Sun Feb 15 03:51:15 CET 2009

Dear Chris, 
Thanks for your reply.
I want to get the figure like the link http://p13.freep.cn/p.aspx?u=v20_p13_p_0902131629052385_0.bmp
So I ran g_spatial and loaded the output.cube into VMD in volumeslice representation. 
I don't know whether the method is practicable to get the figure of the solvent density map.
>	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.
   I do view it as an isosurface.

>>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?
  I also changed the axis and pushed the slice offset bar,but no anything is still viewed

>>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?
 When I ran g_spatial, my processes are those.
 1. my system is one solute and 511 solvent. 
    I use make_ndx to create a group containing the atoms of solvent.
 2. trjconv -s md.tpr -f md.xtc -o md1.xtc -boxcenter tric -ur compact -pbc none
 3. trjconv -s md.tpr -f md1.xtc -o md2.xtc -fit rot+trans
 4. g_spatial -s md.tpr -f md2.xtc -n solvent.ndx -bin 0.1 -nab 300
 5. load grid.cube into VMD

> 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.      
> 				           Jinyao Wang

= = = = = = = = = = = = = = = = = = = = 
        Jinyao Wang
        wangjy at ciac.jl.cn

More information about the gromacs.org_gmx-users mailing list