[gmx-users] Partial density versus time

[Tsjerk Wassenaar]

Hi Faezeh,

According to your previous mail, what you want is...

> I am dealing with phase separation of a two-component system. At the end
of
> simulation the mixed system phase separate to two phases, one is rich in
> one component and the other phase is rich with the other component. So I
> want to see how each component  reachs those fractions by time?

... to see how the components phase separate.

In a maximally mixed state, the number of contacts between species A and B
in the mixture is maximal, while the number of contacts within the groups A
and B, respectively, are minimal. Vice-versa, in a completely phase
separated system, the number of contacts between groups is minimal (only
the interface), while the contacts within groups are maximized. So these
numbers should show you the time course and degree of phase separation,
which seems to be what you stated to want. Apparently, you do not want what
you said you wanted, but maybe we can give it another shot with a
description of what you really want then.

Best,

Tsjerk



On Thu, Apr 7, 2016 at 6:42 PM, Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> Dear Tsjerk, no that does not give what I want.
>
>
>
> Best regards
>
>
> On Thu, Apr 7, 2016 at 6:41 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>
> wrote:
>
> > Hi Negar,
> >
> > I tried your solution, but still it does not give the density (of each
> > component) versus time. It gives density versus distance for different
> > frames. This could be easily done by g_density with an .ndx file. I need
> to
> > have a plot of density-time for each of the components of the system.
> >
> > Please help...
> >
> >
> >
> >
> > Best regards
> >
> >
> > On Wed, Apr 6, 2016 at 7:13 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> >> Hi Faezeh,
> >>
> >> You can count the number of contacts within and between groups to follow
> >> the process over time using gmx mindist.
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >> On Apr 6, 2016 17:10, "Faezeh Pousaneh" <fpoosaneh at gmail.com> wrote:
> >>
> >> > Hi Tsjerk,
> >> >
> >> > Thanks, but my question it is not that simple.
> >> > I am dealing with phase separation of a two-component system. At the
> >> end of
> >> > simulation the mixed system phase separate to two phases, one is rich
> in
> >> > one component and the other phase is rich with the other component.
> So I
> >> > want to see how each component  reachs those fractions by time?
> >> >
> >> >
> >> >
> >> > Best regards
> >> >
> >> >
> >> > On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> >> > wrote:
> >> >
> >> > > Hi Faezeh,
> >> > >
> >> > > Using -b/-e flags you can get the density profile over a window of
> >> time
> >> > (or
> >> > > a single frame). Afterwards you can combine the results to have a
> >> density
> >> > > profile over time.
> >> > >
> >> > > Hope it helps,
> >> > >
> >> > > Tsjerk
> >> > >
> >> > > On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh <
> fpoosaneh at gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Hi,
> >> > > >
> >> > > > Is it possible to obtain partial density versus time in Gromacs?
> >> > > Precisely,
> >> > > > I have a system of two components which separate by time. I need
> the
> >> > > > evolution of density of each phase by time?
> >> > > >
> >> > > > thanks.
> >> > > > Best regards
> >> > > > --
> >> > > > Gromacs Users mailing list
> >> > > >
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> >> > > > posting!
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> >> > > >
> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > Tsjerk A. Wassenaar, Ph.D.
> >> > > --
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> >> > >
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-- 
Tsjerk A. Wassenaar, Ph.D.