[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

[Rasoul Nasiri]

Is there any other (not g_energy) tools in GROMACS to estimate T properly?

Rasoul


On Thu, Jul 10, 2014 at 5:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/10/14, 12:49 PM, Rasoul Nasiri wrote:
>
>> Hi,
>>
>> Can anybody tell me why these two tools give different temperature values
>> based on same trajectory and input files?
>>
>>
>> 1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg
>>
>>       0.000000  508.066786
>>      1.000000  496.066137
>>      2.000000  501.665712
>>      3.000000  498.809896
>>      4.000000  499.838636
>>      5.000000  498.828986
>>      6.000000  500.653778
>>
>>
>> 2- g_traj -f md_shor.trr -s topol_shor.tpr -ot T-.xvg
>>
>>   0      338.107
>>   1      334.99
>>   2      338.707
>>   3      336.785
>>   4      337.642
>>   5      337.062
>>   6      338.132
>>
>>
>> the desired temperature was 500 K in mdp file.
>>
>>
>>
> As stated in the help description, g_traj does not correct for constrained
> degrees of freedom.
>
> -Justin
>
> --
> ==================================================
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> 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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