[gmx-users] Temperature Histogram

[cuong nguyen]

Dear,

Thanks a lot for your suggestion Justin.
I have a box 3 3 20 and want to plot the temperature along the z axis. I
did the commands:
g_energy -f NVT_20ns.edr -s topol.top -o temp
g_analyze -f temp.xvg -dist temp.xvg

and got the results:
  281.9 0  282 0.000149997  282.1 0  282.2 0  282.3 0  282.4 0  282.5 0
282.6 0  282.7 0  282.8 0  282.9 0  283 0  283.1 0  283.2 0  283.3 0  283.4
0  283.5 0  283.6 0  283.7 0.000149997  283.8 0  283.9 0  284 0  284.1
0.000149997  284.2 0  284.3 0.000149997
         .........

I supposed the first column should start from 0 to 20.
Please tell me what's wrong I am doing?

Best regards,

Cuong

On 8 November 2012 01:16, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/7/12 11:42 AM, Samadashvili Nino wrote:
>
>> Hello,
>>
>>    I would like to calculate temperature in my system along the axis.
>> Could you please tell me if there is a way to make a temperature histogram
>> with Gromacs?
>>
>>
> Use g_energy to extract temperatures from the .edr file, then g_analyze
> -dist on that .xvg file.
>
> -Justin
>
> --
> ==============================**==========
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
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