Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Hi Tsjerk

Your approach shows of course the appearance of the phase separation, but I
necessarily need the time evolution of density of one component to see
'how' it reaches the equilibrium obtaining two difference mass fractions.


Best regards.


Best regards


On Fri, Apr 8, 2016 at 12:34 PM, Faezeh Pousaneh 
wrote:

> Hi Tsjerk
>
> I attach a picture what I explicitly want. Your approach shows of course
> the appearance of the phase separation, but I necessarily need the time
> evolution of density of one component to see 'how' it reaches the
> equilibrium by obtaining two difference mass fractions.  .
>
>
> Best regards.
>
>
>
> Best regards
>
>
> On Fri, Apr 8, 2016 at 11:28 AM, Faezeh Pousaneh 
> wrote:
>
>>
>> Hi Tsjerk,
>>
>> I attach a picture what I explicitly want. Your approach shows of course
>> the appearance of the phase separation, but I necessarily need the time
>> evolution of density of one component to see 'how' it reaches the
>> equilibrium by obtaining two difference mass fractions.
>>
>>
>> Best regards
>>
>>
>> On Thu, Apr 7, 2016 at 10:32 PM, Tsjerk Wassenaar 
>> wrote:
>>
>>> 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 
>>> wrote:
>>>
>>> > Dear Tsjerk, no that does not give what I want.
>>> >
>>> >
>>> >
>>> > Best regards
>>> >
>>> >
>>> > On Thu, Apr 7, 2016 at 6:41 PM, Faezeh Pousaneh 
>>> > 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 
>>> > > 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" 
>>> 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 <
>>> tsje...@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 <
>>> > fpoosa...@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.
>>> > >> 

Re: [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  wrote:

> Dear Tsjerk, no that does not give what I want.
>
>
>
> Best regards
>
>
> On Thu, Apr 7, 2016 at 6:41 PM, Faezeh Pousaneh 
> 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 
> > 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"  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 
> >> > 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 <
> fpoosa...@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
> >> > > >
> >> > > > * Please search the archive at
> >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> >> > > > posting!
> >> > > >
> >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> > > >
> >> > > > * For (un)subscribe requests visit
> >> > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> or
> >> > > > send a mail to gmx-users-requ...@gromacs.org.
> >> > > >
> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > Tsjerk A. Wassenaar, Ph.D.
> >> > > --
> >> > > Gromacs Users mailing list
> >> > >
> >> > > * Please search the archive at
> >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > > posting!
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> >> > >
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> or
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> >> > >
> >> > --
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> >> > posting!
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Re: [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  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 
> 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"  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 
>> > 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 
>> > > 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
>> > > >
>> > > > * Please search the archive at
>> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > > posting!
>> > > >
>> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > >
>> > > > * For (un)subscribe requests visit
>> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>> > > > send a mail to gmx-users-requ...@gromacs.org.
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Tsjerk A. Wassenaar, Ph.D.
>> > > --
>> > > Gromacs Users mailing list
>> > >
>> > > * Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > posting!
>> > >
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > > * For (un)subscribe requests visit
>> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > > send a mail to gmx-users-requ...@gromacs.org.
>> > >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
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>> >
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>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>>
>
>
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

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  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"  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 
> > 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 
> > > 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
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] Partial density versus time

[Tsjerk Wassenaar]

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"  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 
> 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 
> > 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
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Thanks alot  Negar!!

I am going to try, I'll ask you if I face with a problem.


Best regards


On Wed, Apr 6, 2016 at 5:09 PM, Negar Ashari Astani 
wrote:

> ... Yes, I guess this can be easily done using Density profile tool of
> VMD. Since you are running classical simulations with gromacs you probably
> have your system topology with different residues and fragments. So you can
> easily choose each phase of your system in selected atoms (a combination of
> residues) and ask for the the density of this phase in the course of
> simulation. You just need to be careful when converting the units, as this
> plugin counts the atoms, thus if you have water molecule, the plugin counts
> that molecule three times (three atoms of the molecule), so you need to put
> "Name O and residue WAT" such that it counts a water molecule only once!
>
> Let me know if you need more explanation,
> Best,
> Negar
>
> On Wed, Apr 6, 2016 at 4:59 PM Faezeh Pousaneh 
> wrote:
>
>> Thanks Negar.
>>
>> More detail; my system phase-separate after equilibrium, such that each
>> component reaches two mole (or mass) fractions. One mole fraction at its
>> rich-phase and one mole fraction at its poor phase. I need to know those
>> two densities or fractions.
>>
>> I do not know your way.  Could you explain me a bit more.
>>
>>
>> Best regards
>>
>>
>> On Wed, Apr 6, 2016 at 4:45 PM, Negar Ashari Astani <
>> negarast...@gmail.com> wrote:
>>
>>>  Just a correction: The main plugin I used is " Density profile
>>> tool" and then for visualization as a volumetric density I used VOLMAP.
>>>
>>> On Wed, Apr 6, 2016 at 4:42 PM Negar Ashari Astani <
>>> negarast...@gmail.com> wrote:
>>>
 Hello Faezeh,

 If by density you mean the mass density, you can use VOLMAP plugin of
 VMD to analyze the density evolution in the course of simulation.
 If this is what you mean, I'll be happy to help with more information.

 Best,
 Negar


 On Wed, Apr 6, 2016 at 4:30 PM Faezeh Pousaneh 
 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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>

>>
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

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  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 
> 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
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Thanks Negar.

More detail; my system phase-separate after equilibrium, such that each
component reaches two mole (or mass) fractions. One mole fraction at its
rich-phase and one mole fraction at its poor phase. I need to know those
two densities or fractions.

I do not know your way.  Could you explain me a bit more.


Best regards


On Wed, Apr 6, 2016 at 4:45 PM, Negar Ashari Astani 
wrote:

>  Just a correction: The main plugin I used is " Density profile tool"
> and then for visualization as a volumetric density I used VOLMAP.
>
> On Wed, Apr 6, 2016 at 4:42 PM Negar Ashari Astani 
> wrote:
>
>> Hello Faezeh,
>>
>> If by density you mean the mass density, you can use VOLMAP plugin of VMD
>> to analyze the density evolution in the course of simulation.
>> If this is what you mean, I'll be happy to help with more information.
>>
>> Best,
>> Negar
>>
>>
>> On Wed, Apr 6, 2016 at 4:30 PM Faezeh Pousaneh 
>> 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
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
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Re: [gmx-users] Partial density versus time

[Tsjerk Wassenaar]

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  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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
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