[gmx-users]site-site radial distribution function

[Payman Pirzadeh]

Hello,

I have two questions about using g_rdf:

 

1.       Is it meaningful to calculate the radial distribution of water
molecules around a single atom of a surface residue, e.g. dangling OG1
oxygen of Threonine? (Does g_rdf takes care of the protein presence and the
excluded volume?)

2.       How will the RDF be calculated in a heterogeneous system? For
instance, if you have protein in a solvent near a solvent's crystal's
surface? What is considered as the bulk density of the solvent? Whole box?

Thanks.

 

Paymon

 

 

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101029/5bad7043/attachment.html>