[gmx-users] How can get the radial atom density profile?

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Aug 24 05:17:29 CEST 2004

>My molecules look like globule so I want to know the density profile along
>the radial direction. Can I use the analysis tool in Gromacs to get it
>directly or should I do some modification about the source code such as the
>g_density part?

There is g_rdf that you can use to generate a radial distribution function.

If you are interested in the density in three dimensions, rather than in 
one, then Christoph made a program, g_sdf, that generates a spatial 
distribution function that you can use to generate nice images showing how 
things are orientated to a molecule/atom (not sure why it didn't make it 
into the general release of GROMACS).  I can send you a file of it that you 
will need to compile to use.  I have hacked the code myself so that it can 
sum the function over multiple molecules.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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