Dear Tsjerk,
Thank you very much from your response.
How do I consider this in my analysis, Please?
Best Regards
Dina
________________________________
From: Tsjerk Wassenaar <tsje...@gmail.com>
To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Friday, April 6, 2012 12:53 PM
Subject: Re: [gmx-users] volume in ensemble
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" <dinadu...@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 RegardsDina
>
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