[gmx-developers] Computing the density of water around water
Anton Feenstra
feenstra at few.vu.nl
Tue Apr 11 21:23:15 CEST 2006
Mark Abraham wrote:
>>Hi,
>>
>> I know that one can get g2(r) (radial distribution) information from a
>>simulation of identical particles by looping over all particles i and
>>making a nested loop over all particles j < i. Thus, one can compute
>>(1/2)N^2 interactions from each snapshot for computing the histograms that
>>go into each g2(r). However, I'm not sure if one can do this for the
>>three-dimensional density calculations.
>> If I simply want to plot the three-dimensional density of water oxygen
>>atoms around a particular water molecule, is it OK to do a simple
>>simulation of water (no constraints, no particle fixed at the center)
>
>
> Of course - you don't need a fixed particle from which to measure. The
> distribution of atom-atom distances is necessarily independent of the
> reference frame in which they are measured. After the fact, you could move
> your box to center it on a particular water at each time step, or you
> could be perverse and have a box that moved around randomly and still all
> the atoms have the same distribution of distances.
You'd want to normalize on the infinitisimal volume, to correct for the
r^2 dependence of the sphere at r you'r integrating over. Check out
g_rdf, it does it that way.
--
Groetjes,
Anton
* NOTE: New Affiliation, Phone & Fax numbers (below) *
_____________ _______________________________________________________
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
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