[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools
Rasoul Nasiri
nasiri1355 at gmail.com
Thu Jul 10 18:58:28 CEST 2014
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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