AMBER Archive (2009)

Subject: Re: [AMBER] density and volume in NVT ensamble

From: Andrew Purkiss-Trew (
Date: Mon Feb 16 2009 - 08:14:40 CST

This is because the density and volume do not appear in the mdout file
and the perl script that processes the file just gives a single column
(time) in the relevant processed files. If you look at summary.VOLUME,
you will see just the time column, compare this with summary.ETOT where
you will see two columns: time and energy.

Your graphs just show the result of plotting x vs x and are a 'feature'
of xmgrace when there is no y data to plot.

On Mon, 2009-02-16 at 15:58 +0200, oguz gurbulak wrote:
> Dear All,
> I run a md in NVT ensamble. And I wanted to see the graphs of density and
> volume with using xmgrace. I realized that both density and volume increase
> at the end of the md. I didn't find what the problem is about my operation.
> Could you help me to learn the reason ?
> MD equilibration
> &cntrl
> imin=0, irest=0, nstlim=10000, dt=0.002, ntx=1,
> ntc=2, ntf=2, ntpr=500, ntwx=500, ntwr=500, ntwe=500, ntwv=500,
> cut=9.825, ntb=1, ntp=0, ntr=0, ntt=1,tautp=2.0, vlimit=5,
> tempi=0.0, temp0=273.0,
> /
> Thank you very much for your attention.
> Kind regards.
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