Fix application tests

Issue Description:

Several application tests are failing. Details:

• CP2K: Failures are due to input file issues.
• NAMD: Need to fix CPU affinity for some CPU-based tests.
• GROMACS: Some tests use the gmx_mpi binary, but on certain versions, only the double-precision binary was compiled. As a result, the tests fail because the expected binary is not found.

FAILURE INFO for Gromacs_plumed_pocr %modules_infos=('adastra:cpu', 'GCC-CPU-3.1.0', 'gromacs/2023.3-cp2k-omp-plumed-mpi') (run: 1/1)
  * Description: Gromacs application test
  * System partition: adastra:cpu
  * Environment: GCC-CPU-3.1.0
  * Test file: /lus/home/BCINES/dci/jourdain/test/cines-reframe-tests/checks/apps/gromacs/reframe_gromacs_plumed_pocr.py
  * Stage directory: /lus/home/BCINES/dci/jourdain/test/cines-reframe-tests/stage/adastra/cpu/GCC-CPU-3.1.0/Gromacs_plumed_pocr_a92d094d
  * Node list: c1524
  * Job type: batch job (id=4271795)
  * Dependencies (conceptual): []
  * Dependencies (actual): []
  * Maintainers: []
  * Failing phase: sanity
  * Rerun with '-n /a92d094d -p GCC-CPU-3.1.0 --system adastra -r'
  * Reason: sanity error: pattern 'Performance:' not found in 'rfm_job.err'
--- rfm_job.out (last 10 lines) ---

-----------------------------------------------------------



CINES Job Report:

-----------------

 --- rfm_job.out ---
--- rfm_job.err (last 10 lines) ---
slurmstepd: error: execve(): gmx_mpi: No such file or directory
slurmstepd: error: execve(): gmx_mpi: No such file or directory
slurmstepd: error: execve(): gmx_mpi: No such file or directory
slurmstepd: error: execve(): gmx_mpi: No such file or directory
srun: error: c1524: tasks 0-47: Exited with exit code 2