[gmx-users] pressure-lyzozyme tutorial

delara aghaie d_aghaie at yahoo.com
Sat Jun 16 16:08:18 CEST 2012

Dear Justin
Many Thanks. The correspondence between statistical mechanics and simulation results is beautiful :)

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: delara aghaie <d_aghaie at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 June 2012, 18:12
Subject: Re: [gmx-users] pressure-lyzozyme tutorial

On 6/16/12 9:40 AM, delara aghaie wrote:
> Dear Gromacs users
> 1)) I want to know a way to have running averages on plots. I usually draw my
> plots using gnuplot.
> In Lyzozyme tutorial, we see a graph for pressure. ( I want to have something
> like that)

I used XmGrace for that plot, as well as everything else I do, so I can't 
comment on this question.

> 2)) in that tutorial, The average press is about 1 bar, but the fluctuations of
> the pressure reach 200 and -200 bar. Is it correct to say the pressure is 1 bar,
> when we see these great fluctuations?...

Please read http://www.gromacs.org/Documentation/Terminology/Pressure.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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