AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Feb 16 2009 - 08:04:22 CST

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_at_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.
>
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>
>

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