[gmx-users] Temperature output file

[Vitaly V. Chaban]

Temperature groups have to be defined in the parameter file to derive the
coveted data, I believe.





On Thu, Oct 22, 2015 at 11:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/22/15 9:01 AM, Ali Mohyeddin wrote:
>
>> Dear all,
>>
>> I am very beginner to gromacs. I have already simulated a simple protein
>> using a nice gromacs tutorial.
>> (
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
>> )
>> Now I want to run some analysis to get the temperatures of protein and
>> solvent separately. I have entered the following command but nothing
>> written in temperature.xvg file:
>>
>> gmx traj  -f  md_0_1.xtc  -s  md_0_1.tpr  -ot  temperature.xvg
>>
>> May anyone help me?
>>
>>
> There are no velocities in an .xtc file, so temperature can't be
> calculated. Moreover, you have to correct for the influence of constraints.
>
> Simply put, you're using the wrong program for something simple like
> this.  What you want is gmx energy, as all temperature data are stored in
> the .edr file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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