[gmx-users] Re: RDF - water and protein

Thomas Schlesier schlesi at uni-mainz.de
Mon May 13 18:07:08 CEST 2013

the manual mentions that with the option '-surf' no normalization is 
done. So it's normal the RDF will inrease with larger distances, since 
the further you'll go away from the protein, the bigger the spherical 
shell is (from which the RDF for distance r is calculated) and the more 
water molecules will be in this shell.

Because of this using the '-nopbc' option shouldn't change anything.
One thing which i find rather strange, is that for really high distances 
the RDF goes down. Would have thought that with pbc the RDF should 
increase all the time.

But i have no idea to perform a sensible normalization afterwards.


Am 13.05.2013 17:24, schrieb gmx-users-request at gromacs.org:
> Dear Gmx Users,
> I run long simulation of my protein with 50 small molecules in water.
> I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com.
> Please, take a look at my plot:
> http://speedy.sh/tmJbD/rdf-P-W.png
> Could you please, explain me why the second peak is so high? Shall I use
> option -nopbc ?
> How can I obtain the density [kg/m3] versus the distance? I wish to compare
> it with RDF of Protein-Ligands so wish to use some normalization for them
> to be comparable - peaks will be visible.
> Steven

More information about the gromacs.org_gmx-users mailing list