# System does not reach designated temperature after NVT runs **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [October 19, 2022, 3:32am UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055 "2022-10-19T03:32:37Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![lcheng](https://avatars.discourse-cdn.com/v4/letter/l/9fc348/32.png) [@lcheng](https://gromacs.bioexcel.eu/u/lcheng)\ **Post date:** [October 19, 2022, 3:32am UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/1 "2022-10-19T03:32:37Z")
GROMACS version: GROMACS modification: Yes/No Hi, I am trying to run a MD simulation for a protein-ligand system. I set the temperature to be 323.25 K but the temperature after NVT running only reaches around 223K. Here is my nvt.mdp file. I appreciate for any feedbacks. title = Protein-ligand complex NVT equilibration define = -DPOSRES ; Run parameters integrator = md nsteps = 50000 dt = 0.002 ; Output control nstenergy = 500 nstlog = 500 nstxout-compressed = 500 nstvout = 500 ; Bond parameters continuation = no constraint\_algorithm = lincs constraints = h-bonds lincs\_iter = 1 lincs\_order = 4 ; Neighbor searching and vdW cutoff-scheme = Verlet ns\_type = grid nstlist = 20 rlist = 1.2 vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; Electrostatics coulombtype = PME rcoulomb = 1.2 pme\_order = 4 fourierspacing = 0.16 ; Temperature coupling tcoupl = V-rescale tc-grps = Protein\_PLT Water\_and\_ions tau\_t = 0.1 0.1 ref\_t = 323.25 323.25 comm-grps = Protein\_PLT Water\_and\_ions comm-mode = Angular ; Pressure coupling pcoupl = no ; Periodic boundary conditions pbc = xyz ; Dispersion correction is not used for proteins with the C36 additive FF DispCorr = no ; Velocity generation gen\_vel = yes gen\_temp = 323.25 gen\_seed = -1 ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [October 19, 2022, 12:54pm UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/2 "2022-10-19T12:54:11Z")
Where did you get the temperature of 223 K from? Note that you should not use angular COMM removal on the solvent. ---
**Author:** ![nano](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@nano](https://gromacs.bioexcel.eu/u/nano)\ **Post date:** [October 19, 2022, 4:30pm UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/3 "2022-10-19T16:30:39Z")
Directly from _gmx energy_, I guess. But these do not exclude constraints, and thus not the “right” value. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [October 19, 2022, 4:53pm UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/4 "2022-10-19T16:53:08Z")
`gmx energy` explicitly _does_ account for constraints and reports a correct temperature. The output of `gmx traj` from velocities requires correction based on constraints. ---
**Author:** ![lcheng](https://avatars.discourse-cdn.com/v4/letter/l/9fc348/32.png) [@lcheng](https://gromacs.bioexcel.eu/u/lcheng)\ **Post date:** [October 19, 2022, 5:03pm UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/5 "2022-10-19T17:03:19Z")
Thanks for your reply. I got the value from gmx traj. Do you mean I need to remove this term: comm-mode = Angular? ---
**Author:** ![lcheng](https://avatars.discourse-cdn.com/v4/letter/l/9fc348/32.png) [@lcheng](https://gromacs.bioexcel.eu/u/lcheng)\ **Post date:** [October 19, 2022, 5:03pm UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/6 "2022-10-19T17:03:52Z")
Thank you! I got the value from gmx traj and that’ s probably the reason ---
**Author:** ![nano](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@nano](https://gromacs.bioexcel.eu/u/nano)\ **Post date:** [October 19, 2022, 8:31pm UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/7 "2022-10-19T20:31:27Z")
My bad for my poor memory which was quite a while ago when I had the same confusion. Thanks for the clarification! ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [October 20, 2022, 8:38am UTC](https://gromacs.bioexcel.eu/t/system-does-not-reach-designated-temperature-after-nvt-runs/5055/8 "2022-10-20T08:38:13Z")
You should not get the temperature from gmx traj as that does not know about constraints, as the help says. You should use gmx energy. You temperature is very likely correct. If you don’t know why you are using comm-mode=angular, you should not be using it. It is also better to use only one group, the system, for COMM removal.