[gmx-users] rdf between com of molecules

[Anton Feenstra]

hagop demirdjian wrote:
> 
> 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).

Thanks :-)

> 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 ?

How large (or small!) is the difference between the COM of a water
molecule and the position of the oxygen? The hydrogens are close anyway,
and have only 1/16 the mass, so it can't differ by much more than
.01 nm...

If you *really*really* want it, it's simplest to dive into the 
source code for g_rdf yourself.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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