[gmx-users] Time series of the number of atoms with the volume

[Mark Abraham]

Hi,

On Sun, Jul 22, 2018, 14:15 Mijiddorj B <b.mijiddorj at gmail.com> wrote:

> Dear Mark,
> Thank you bery much for your reply. I do not know which tool is useful for
> the counting a time series of atom number.


Me neither, but first you need to have made the selections of atoms to
count. Maybe gmx select or gmx analyze will help. But you need to do your
own reading of the documentation, too!

I think that gmx select is a
> possible one. However, I could not specify water molecules.
> If you have any experience of gmx select ... , please advise me on
> specifing water molecules using z coordinates.
>

My experience is only that you should look at the examples ;-)

Mark

Best regards,
> Miji
>
> >
> >
> > Message: 4
> > Date: Sat, 21 Jul 2018 19:56:07 +0200
> > From: Mark Abraham <mark.j.abraham at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
> >         <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Subject: Re: [gmx-users] Time series of the number of atoms with the
> >         volume
> > Message-ID:
> >         <CAMNuMAR-7B696e0E5xqJpruErB4_OMz2u=
> > EGri+aLoTPMf-oog at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi,
> >
> > There's quite a few examples in its documentation, do look there for
> ideas.
> > You will need to decide some geometric criterion to define the volume of
> > the pore.
> >
> > Mark
> >
> > On Sat, Jul 21, 2018, 16:27 Mijiddorj B <b.mijiddorj at gmail.com> wrote:
> >
> > > Dear GMX users,
> > >
> > > I would like to make analysis of atom numbers within the certain volume
> > > such as pore of channel. If you have any experience, please advise me.
> > > How can I use gmx select for this purpose?
> > >
> > > Best regards,
> > > Miji
> > > --
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