[gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

[ISHRAT JAHAN]

sorry i did not get what you said...
actually i want to calculate distribution of water at various distance
around backbone as done in paper "Regulation and aggregation of
intrinsically disordered peptides" by Zachary A.Levine et.al.



On Mon, Apr 3, 2017 at 1:54 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> So, you want to make a selection according to a geometric criterion, which
> is what gmx select does.
>
> Mark
>
> On Mon, Apr 3, 2017 at 10:12 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
>
> > i want to calculate number of water molecule within given distance from
> > protein.
> >
> >
> > On Mon, Apr 3, 2017 at 1:20 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > It's not clear to me what you actually want, or why trjorder is even a
> > > possible tool for the job. Look at
> > > http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html
> and
> > > find something useful.
> > >
> > > Mark
> > >
> > > On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN <jishrat17 at gmail.com>
> wrote:
> > >
> > > > ---------- Forwarded message ----------
> > > > From: ISHRAT JAHAN <jishrat17 at gmail.com>
> > > > Date: Fri, Mar 31, 2017 at 12:51 PM
> > > > Subject: analysis of osmolyte at particular distance from backbone
> > > > To: gmx-users at gromacs.org
> > > >
> > > >
> > > > Dear all,
> > > >
> > > > I want to calculate the number of osmolyte molecule at particular
> > > distance
> > > > from backbone with respect to residue.I have tried the command
> trjorder
> > > but
> > > > it gives the number of osmolytes w.r.t time and i want it w.r.t
> > residue.
> > > > Can anyone help me how to calculate this.
> > > > Thanks in advance
> > > > --
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