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

[Anh Mai]

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.
Thanks a lot.

Sincerely yours,
Anh Mai