these files have no density or volume in them, so I think the other
suggestion is correct, that you are trying to extract data that
doesn't exist. always look carefully at your outputs and try to
understand them, don't rely on an analysis script that someone else
wrote without looking at the output, especially if the results don't
make sense. look at your analysis- where are the volume and density
supposed to be coming from?
On Mon, Feb 16, 2009 at 9:27 AM, oguz gurbulak <gurbulakoguz.gmail.com> wrote:
> 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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Received on Wed Feb 18 2009 - 01:09:52 PST
