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.
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Lab: 303 Engel Hall
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