[gmx-users] g_spatial and vmd volume slice (was "chris")

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Feb 15 18:58:16 CET 2009

Dear Jinyao,

1. Your usage of trjconv prior to g_spatial is incorrect.
trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
Since you didn't center your atoms of interest, you will not get good results.

2. what happens when you run g_spatial? Do you get some strange notes  
or warnings? In 4.0.x, g_spatial was overwritten by g_cluster, so you  
may not actually be runnin g_spatial at all -- try g_spatial -h and if  
you get a notice about g_cluster then you know that this is the case.

3. try doing this with only one frame (use a .gro instead of a .xtc)  
and apply -bin 0.5. If that doesn't work then you dinfinately have  
something else wrong.

4. If you still have problems, please try all of the suggestions that  
I made for you in the first post and report back. I spent some time on  
that and it makes me wonder why you didn't bother to test those  

Also, please keep the subject the same.


--- original message ---

Dear Chris,
Thanks for your reply.
I want to get the figure like the link  
So I ran g_spatial and loaded the output.cube into VMD in volumeslice  
I don't know whether the method is practicable to get the figure of  
the solvent density map.

[Hide Quoted Text]

         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

[Hide Quoted Text]

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

[Hide Quoted Text]

¡¡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

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