[gmx-users] volume in ensemble

dina dusti dinadusti at yahoo.com
Fri Apr 6 12:21:45 CEST 2012

Dear Tsjerk,

Thank you very much from your response.
How do I consider this in my analysis, Please?

Best Regards

 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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. 
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 RegardsDina
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