[gmx-users] g_rdf query

[Mark Abraham]

On 2/06/2011 5:52 PM, Anirban Ghosh wrote:
>
> Hi ALL,
>
> I am using in calculating the distribution of a solvent around the COM
> of a protein chain using g_rdf. When I plot the output file (attached)
> I get a curve which increases first (from 1 to a value of about 2.5)
> and then decreases to x-axis values ranging from 1 to 5. If I
> understand correctly then x-axis values represent the radius of
> calculation around the protein. right? It says "r". Whats its unit?

See chapter 2 of the manual.

> And what does the y-axis values stand for? Can someone please explain
> me the g_rdf plot attached here.
> Thanks a lot in advance.

It means what the y-axis normally means in a distribution (or frequency) 
plot. The absolute magnitude of the values is unimportant, except 
inasmuch as they determine how the integral is interpreted (and vice-versa).

Mark