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

[Mark Abraham]

Hi,

Some of those tools calculate distribution functions. Please start by
looking at them and seeing if they seem suitable.

Mark

On Mon, Apr 3, 2017 at 11:59 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> 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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