[gmx-users] Re:Re: g_spatial and vmd volume slice

XAvier Periole x.periole at rug.nl
Tue Feb 17 09:58:51 CET 2009

>  1. My solute molecule is planar molecule. When I load my *.cube  
> file to VMD, the solute molecule is not perpendicular to any axis.
your question is not clear! You may reorient your solute prior giving  
it to VMD.
Some gmx tools allow to do this. you could fit to a reference  
structure that is it self
oriented along an axis of your choice.
>  2. How to set color labels in the volumeslice to show the color  
> scale coorresponding to the bulk concentration.
I have played with this recently and could not find the way to set or  
change the colors on the volume
slice. I am not sure this is possible. Moreover I found that the  
colors, although clearly showing the
expected pattern for the data plotted, it was also having strange  
behavior: it was giving a color to
certain regions that was not representative of the values.
>  3. In your last email, I have some questions.
>> 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.
>  You are right. Is your meaning that I shound run trjconv like that?
>   trjconv -s a.tpr -f a.xtc -o b.xtc -center -ur compact -pbc none.
>> 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.
> I have known it. When I set up the GMX3.3.3, I have corrected it.
>> 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.
> Why try one frame?
>> 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
>> suggestions.
>> Also, please keep the subject the same.
>> Chris
>> --- original message ---
>> 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.
>> [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]
>> Chris.
>>  Hi gmx-users,
>> I want to get a solvent density map like that in the link
>> http://p13.freep.cn/p.aspx?u=v20_p13_p_0902131629052385_0.bmp
>> 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
>           2009-02-17
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