[gmx-users] Partial density versus time

[Faezeh Pousaneh]

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