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

[Mark Abraham]

Hi,

I suggest you don't ask for "within 0.5 of com of protein" if what you want
is e.g. "within 0.5 of protein"

Mark

On Mon, Jan 21, 2019 at 3:51 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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