[gmx-users] volume in ensemble

[Tsjerk Wassenaar]

Hi Dina,

In your experiments your volume doesn't change (significantly). But if you
were to carve out a very small cube around a micelle, and track the
molecules in there (neglecting diffusion), you'd see that the molecules
sometimes expand and sometimes contract. That's what's happening on a
microscopic scale. And that's what you should be considering in your
analysis: a system with (local) fluctuations in density.

Cheers,

Tsjerk

On Apr 6, 2012 9:41 AM, "dina dusti" <dinadusti at yahoo.com> wrote:

Dear GROMACS Specialists,

May I ask you to answer my question, Please?

I  have several systems consist of water and different molecules
(surfactant and etc. with same molecule number in all of them except
water)  that equilibrated them in NPT ensemble, I wanted to have all of
systems with same volume, so adjusted their volume by variation of water
molecules in each system and after equilibration, volume for all of them
was same. (the same as experiment in laboratory)
After product simulation (NPT), volume for all of them changed, it is right
but when I want to calculate density from center of mass of micelle by RDF,
I need to volume that is different for each of systems. Is this a problem
for me, when comparison of systems?
On the other hand, when I do product simulation in NVT ensemble, pressure
change very much relation to P=1atm in equilibrium.

Please help me.
Thank you very much in advance.
Best Regards
Dina

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