[gmx-users] Partial density versus time

Faezeh Pousaneh fpoosaneh at gmail.com
Thu Apr 7 18:42:20 CEST 2016


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
> > > > --
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> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
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