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

[Justin Lemkul]

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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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