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

dbiswal at ucalgary.ca dbiswal at ucalgary.ca
Wed Aug 3 01:49:46 CEST 2011

 Thanks Chris. I presume g_sdf won't be helpful for my system.

> 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.
> Chris.
> -- 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)
> regards,
> Debasmita
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