[gmx-users] HB analysis at surfaces

[Eudes Fileti]

Hello Zarrini, thank you very much for the answer.

Unfortunately g_density is not the right tool. With it for example it is
not possible to visualize the characteristic peaks of the formation of the
hydrogen bond in the distribution O ... H. This is because g_density does
not parse pairs but rather the amount of atoms in a slice of the box.

Figure 5 from this paper 10.1021/la803324x shows the analysis that I would
like to do. If I'm not mistaken, the authors used a hacked g_rdf tool to
construct it. I even tried to contact them directly but I got no response.

Bests
eef

_______________________________________
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014

>
> ------------------------------
>
> Message: 5
> Date: Fri, 27 Jan 2017 20:19:25 +0100
> From: Salman Zarrini <salman.zarrini at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] HB analysis at surfaces
> Message-ID:
>         <CAD6yk5DQ6LgHBysfAOMcBfE7RxfPRwouEp1TGhOMQLMgN34JwA at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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
> desire.
>
> gmx density -f case.trr -s case.tpr -n index.ndx -d Z -dens mass -o WD.xvg
> -b 10000 -sl 5000
>
>
> Cheers,
>
> S.Zarrini
>
>
> 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 Ci?ncia e Tecnologia da UNIFESP
> > Av. Cesar Lattes, 1201, Eug?nio de Mello, SP, 12247-014
> > --
>