[gmx-users] rdf between com of molecules

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 18 19:02:47 CET 2002

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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