[gmx-users] protein water rdf with coordination number
jalemkul at vt.edu
Mon May 20 14:36:30 CEST 2019
On 5/19/19 7:11 PM, Dallas Warren wrote:
> RDF ->
> Coordination number ->
> Will need to integrate the g(r) with radius, using the particle
> average density across the box.
Also note that gmx rdf makes no attempt to account for excluded volume
of solute molecules like proteins, so I don't think you can even get a
quantitatively correct coordination number from it in a case like this.
For a homogeneous system, it works fine, but not when there's some
large, irregularly shaped object in the way.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
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