[gmx-users] spatial distribution function in a binary solvent mixture

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Aug 3 00:57:32 CEST 2011

I think that you have a misconception about what g_spatial does. For a  
system with many type A and many type B, you need to average over all  
of one type as the central solute to compute an rdf, and perhaps that  
is what you want for your sdf. g_spatial, however, does not do any  
fitting. g_sdf did that. You can obtain an old version of the source  
(4.0.7 should have it I think) if you want to use g_sdf. I have never  
used g_sdf myself.

In case that doesn't answer your question, then let me make one more point:

g_spatial requires that a bin exists for every count. Thus either (a)  
find a large memory node somewhere or (b) pre-process your trajectory  
using trjorder to order the solvent molecules and then keep only the N  
closest, then run g_spatial. But again, I think that this will not  
provide what you are looking for but is likely to give you a smear  
over your box.


-- original message --

   Dear all,

  I'm working with a binary solvent mixture containing 2000 molecules (1800
  type-A + 200 type-B). Both the types of solvent molecules have similar
structure (they are both diatomic molecules) except the polarity.I'm
trying to calculate sdf of type-B solvent molecules. I followed the
step-by-step instructions from the manual using g_spatial.
  I'm trying to reduce the bin width to 0.05A. The *.cube file generated
with a bin width of 0.09A is already 4.9GB in size. As I'm more
interested in the first solvation shell around the type-B solvent
molecule, I was wondering if I could find a way to control the maximum
radius of the sphere around central molecule (center of coordinates?)?
Also, can anyone please let me know how g_spatial deals with the angular
part of sdf?

(I've searched a lot but could not gather enough meaningful information)


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