[gmx-users] g_rdf

[Christoph Freudenberger]

Hi Kay.

I'm not sure whether I understood you problem correctly, but if you
want to study solvation around parts of a protein in angular dependence
you might want to consinder using spatial distribution functions (SDF).
I have written a tool to calculate SDF's from gmx trajectories.

Tell me if you want to try it. I will provide the source code.

Kay Gottschalk wrote:
> 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/       |
>> |             | "If You See Me Getting High, Knock Me Down"           |
>> |             | (Red Hot Chili Peppers)                               |
>> |_____________|_______________________________________________________|
>>
>>
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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
> 
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-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785