[gmx-users] rdf between com of molecules

[David van der Spoel]

On Mon, 18 Mar 2002, hagop demirdjian wrote:

>Is it possible to compute the Radial Distribution Function of the center 
>of mass of the water molecules for the ion ?
>
>the com option of g_rdf considers the com of ALL the water molecules. 
>The best I could do was build an index group with the Oxygens and get a 
>rdf of those.
>
>Should I define a new topology with a dummy atom at the com of water ? I 
>would then have to rerun all my calculations and I'll be able to define 
>a new group consisting in the coms...
>Is there a better way ?
Probably not straight ahead, but either a minor modification of g_rdf 
might do the trick, or you can do an rdf with all water atoms, which is 
more like what scattering experiments would give.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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