[gmx-users] rdf between com of molecules

hagop demirdjian hagop.demirdjian at ens.fr
Mon Mar 18 15:01:37 CET 2002

Hello, I am a second year phD student and have been using GROMACS for a 
month now to simulate sodium ion in spc water.

Everything works fine and I would like to thank you for your work (the 
constraint force routine was especially useful to me since I compute 
transmission coefficient for rate constants).

I have one question though :

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 ?

Thank you,

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