[gmx-users] rdf between com of molecules
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 ?
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