[gmx-users] Water molecule in the first hydration shell

[ISHRAT JAHAN]

Thanks for the reply Justin sir.Please tell me the right command as i have
to calculate it from the surface of protein.

On Mon, Jan 21, 2019, 1:39 AM Justin Lemkul <jalemkul at vt.edu wrote:

>
>
> On 1/20/19 1:01 AM, ISHRAT JAHAN wrote:
> > Dear all,
> > I want to calculate the number of water molecule within 5 A of protein
> > throughout the trajectory. I have calculated it using the command-
> >    gmx select -n water.ndx -select 'group "water" and within 0.5 of com
> of
> > group "Protein" -os out.xvg  -f  pbc.xtc -s  200ns.tpr -b 110 -tu ns
>
> This selection will give you waters within 5 A of the center-of-mass of
> the protein, which will not encompass the hydration shell.
>
> -Justin
>
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