[gmx-users] g_rdf

[Anton Feenstra]

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 |
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