[gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy"

[Justin Lemkul]

On 2/26/20 8:10 PM, Anh Mai wrote:
> Hi all,
> Could someone please help me?
>
> I have a question about the *temperature outputs *from the two
> packages "gmx traj"
> and "gmx energy."
>
> I used the two packages to export the Temperature of a "Protein" group.
> Here is what I did.
>
>     1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot
>     Temperature_traj.xvg
>     gmx analyze -f Temperature_traj.xvg
>     *Found: Temperature_traj = 250.475 K*
>     2. gmx energy -f energy.edr
>     Select "14 Temperature".
>     *Found: Temperature_energy = 300.137 K*
>
> Our *parameters.mdp* file has:
> "...
> constraints         =  h-bonds
> constraint_algorithm     = Lincs
>
> tc-grps    =  System ; sd integrator (!)
> tau_t               =  2.0 ; sd integrator (!)
> ref_t               =  300
>
> gen_vel             =  yes
> gen_temp    =  300.0
> gen_seed    =  173529
> ..."
>
> I don't know why the two temperatures are that much different from each
> other, such as by 50 degrees.
> Looking forward to an explanation.

gmx traj knows nothing about constraints so the number of degrees of 
freedom for the calculation are incorrect.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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