[gmx-users] g_spatial and vmd volume slice

Chris Neale chris.neale at utoronto.ca
Tue Feb 17 20:23:57 CET 2009

Dear Jinyao,

this is quickly becoming a vmd-mailing list question, but I'll give it 
one more set of replies. I would appreciate if you would coallate these 
into a single how-to and put it on the gromacs wiki once you have 
figured out how to do it.

 >Dear chris,
 >  Thank you for you help.
 > I have solved my problem. If I use VMD at XP system,the volumeslice 
is displayed.
 > I am apologized it that I still have some difficulties to bother you.
 >  1. My solute molecule is planar molecule. When I load my *.cube file 
to VMD, the solute molecule is not perpendicular to any axis.

trjconv -princ or -rotate, look at the structure and repeat with new 
values of rotate until it is aligned how you want.

 >  2. How to set color labels in the volumeslice to show the color 
scale coorresponding to the bulk concentration.

Colour labels? Don't know. To change the color:
a) representation volumeslice
b) graphics--> represenations --> change coloring method to "volume"
c) graphics-->colors-> color scales --> change to white/black
d) graphics-->colors-> color scales --> slide the offset and midpoint 
until you see the level of detail that you want
e) render this and take it to gimp or photoshop, change the background 
to transparent, false color the density that remains, and overlay it on 
a white background or perhaps overlay it on an exactly scaled picture of 
one representative conformation (you can do this exactly by loading in 
the correct structure along with the .cuge file to vmd and changing the 
representation to output two separate files at exactly the same 

 >  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.

Yes, since this is copied directly from g_spatial -h.

 >> >
 >> >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.

Good. I am happy to note that this has been fixed in gmx 4.0.4.

 >> >
 >> >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?

I leave that to you.


 >> >
 >> >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

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