I did what you said , but again I saw the same result ( both density and
volume increase at the end of the md ) . I attached the equ.out to the mail.
Thank you very much for your attention.
Kind regards.
2009/2/16 Carlos Simmerling <carlos.simmerling.gmail.com>
> your density and volume plots look the same.
> you should not see volume changes with ntb=1. it's impossible to tell
> if the problem is in your plots, your data extraction from the mdout,
> or sander. maybe you could copy and paste the relevant output directly
> from sander? paste in the average and rms sections from the end of the
> run. also tell us exactly how you got these values for plotting.
>
>
>
> On Mon, Feb 16, 2009 at 8:58 AM, oguz gurbulak <gurbulakoguz.gmail.com>
> 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.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
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Received on Wed Feb 18 2009 - 01:09:46 PST
