[gmx-users] protein water rdf with coordination number

Justin Lemkul jalemkul at vt.edu
Mon May 20 14:36:30 CEST 2019

On 5/19/19 7:11 PM, Dallas Warren wrote:
> RDF ->
> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html
> Coordination number ->
> https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions
> 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.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list