[gmx-users] g_rdf

[Kay Gottschalk]

I have read in the literature that people calculate the rdf of water 
around single water exposed protein atoms (for example to find the 
difference in the hydration shell around carbons and oxygens).  I want 
to do something comparable to that. Now if I just take g_rdf and one 
protein atom which is solvent exposed, I think that g_rdf normalizes 
the number of water molecules that are close to my reference atom 
according to the number that is expected in a sphere with a certain 
radius around the atom with respect to the density of normal water. The 
problem is that most of the atoms' environment is not solvent, but 
other protein atoms. g_rdf therefore finds much less water molecules 
than expected. I believe that I have to compensate for the volume 
around my reference atom that is inaccessible to water. And I don't 
know how to do it.
Hope my problem is stated more clearly now - if not, complain...
Thanks,
Kay.

On Wednesday, August 6, 2003, at 07:06 PM, Anton Feenstra wrote:

> Kay Gottschalk wrote:
>> No problem with manual:) I'd just like to know how people do the rdf 
>> for single surface atoms. There must be some correction for the 
>> protein volume (which excludes water of course) in the sphere-section 
>> for which the density function is calculated. Is there a clever way 
>> to do that in Gromacs? Actually, I am not sure I am making myself 
>> clear here... At any rate, suggestions would be highly appreciated.
>
> You'll have to do some explaining here ;-(
>
> We've used rdf's (in the past) for comparison with e.g. neutron 
> scattering
> for e.g. water. The angle dependence was added to analyze coordination
> shell structure in liquid water. So, no surfaces there, and no protein.
>
> What do you mean by 'single surface atom', and what correction for 
> protein
> volume should there be? It may be that g_sas has an option to calculate
> the protein surface as well as the volume, but it has been upgraded 
> since
> I last used it so I'm not sure.
>
>
> -- 
> Groetjes,
>
> Anton
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel