[gmx-users] HB analysis at surfaces

Salman Zarrini salman.zarrini at gmail.com
Fri Jan 27 20:20:08 CET 2017

If you mean water profile density then "gmx density" is your friend. Just
invoke below command and play around with the variables to reach your

gmx density -f case.trr -s case.tpr -n index.ndx -d Z -dens mass -o WD.xvg
-b 10000 -sl 5000



On Fri, Jan 27, 2017 at 5:18 PM, Eudes Fileti <fileti at gmail.com> wrote:

> Hello everyone,
> I'm interested in calculating distributions of O...H pairs between water
> and a hydrophilic surface. For this I need a tool that allows the
> calculation of a "g(z)" (that is, a rdf that is not radial, but rather
> depends only on the distance z to the surface).
> Anyone have this tool ready? If not, can anyone suggest me how and which
> gmx tool I could change to achieve this?
> Bests
> _______________________________________
> Eudes Eterno Fileti
> Instituto de Ciência e Tecnologia da UNIFESP
> Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014
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