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

[ISHRAT JAHAN]

I have calculated it and from there i got the forst hydration layer.

On Mon, Jan 21, 2019, 8:29 AM Bratin Kumar Das <177cy500.bratin at nitk.edu.in
wrote:

> Calculate the rdf first
>
> On Mon 21 Jan, 2019, 8:22 AM ISHRAT JAHAN <jishrat17 at gmail.com wrote:
>
> > 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
> > >
> > > --
> > > ==================================================
> > >
> > > 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
> > > http://www.thelemkullab.com
> > >
> > > ==================================================
> > >
> > > --
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