Dear Andrew,
Thank you very much for your attention. But what should I do in my
md.ininput file to see the density and volume information in md.out
file.
Kind regards.
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,
/
2009/2/16 Andrew Purkiss-Trew <a.purkiss.mail.cryst.bbk.ac.uk>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Feb 18 2009 - 01:10:04 PST
