:-) GROMACS - gmx mdrun, 2024.5-conda_forge (-:

Executable:   /hpc2hdd/home/jyang577/miniconda3/envs/gmx-lite/bin.AVX2_256/gmx
Data prefix:  /hpc2hdd/home/jyang577/miniconda3/envs/gmx-lite
Working dir:  /hpc2hdd/home/jyang577/jasperyeoh/TUB-CPPF/yfeng494_data/CPPF+alpha
Command line:
  gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append -v -nb gpu -pme gpu -bonded gpu -ntmpi 1 -ntomp 4

Compiled SIMD is AVX2_256, but CPU also supports AVX_512 (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file md_0_1.tpr, VERSION 2023.2 (single precision)
Note: file tpx version 129, software tpx version 134
Changing nstlist from 10 to 100, rlist from 1.4 to 1.537

Update groups can not be used for this system because there are three or more consecutively coupled constraints

1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 4 OpenMP threads 


NOTE: OS CPU limit is lower than logical cpu count, thread pinning disabled.
starting mdrun 'TUBULIN ALPHA-1B CHAIN in water'
25000000 steps,  50000.0 ps (continuing from step 25000000,  50000.0 ps).

Writing final coordinates.

Back Off! I just backed up md_0_1.gro to ./#md_0_1.gro.1#

step 25000000, remaining wall clock time:     0 s          
NOTE: 18 % of the run time was spent in pair search,
      you might want to increase nstlist (this has no effect on accuracy)

               Core t (s)   Wall t (s)        (%)
       Time:        0.970        0.245      395.6
                 (ns/day)    (hour/ns)
Performance:        0.704       34.070

GROMACS reminds you: "If it's all right with Dirac, it's all right with me." (Enrico Fermi, on being told that there was experimental evidence He-3 nuclei obey Fermi-Dirac statistics.)