[gmx-users] Partial density versus time

Faezeh Pousaneh fpoosaneh at gmail.com
Wed Apr 6 17:16:49 CEST 2016


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 <negarastani at gmail.com>
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 <fpoosaneh at gmail.com>
> 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 <
>> negarastani at 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 <
>>> negarastani at 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 <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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>>>>
>>


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