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 oguz gurbulak <gurbulakoguz.gmail.com>
> 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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>>
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- application/octet-stream attachment: equ.out
Received on Wed Feb 18 2009 - 01:09:48 PST
