Gmx mdrun is too slow for my cpu

I am happy to help, I have spent my fair amount of time trying to solve similar issues, and it can be agonizing at the beginning :)

From what I see in the picture, you did not run -DGMX_GPU=OFF, you just ommited it. I am guessing that either by default or because it detects your GPU, cmake is trying to use a default -DGMX_GPU=ON setting, but because you dont have CUDA installed it raises an error. CUDA is basically a set of tools that allows programs to use your GPU to compute things. It can result in quite a speed-up in some applications, such as MD.

Also, I see that you are still using the 5.1.1 version of GROMACS despite Justin and Paul’s advice. You really should not do that, it is less efficient than newer versions, and it probably is not supported (some errors that you might have have been corrected in newer versions).

Download the newest GROMACS source

and run these commands in the same directory as your downloaded file

tar xfz gromacs-2020.2.tgz
cd gromacs-2020.2
mkdir build-gromacs
cd build-gromacs
cmake .. -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2020.1/

make -j 4
make check -j 4
make install 

OR if the last command complains about permissions,

sudo make install

One last thing, if you run into trouble and want to start again, it is best to delete the whole folder and start from the tar xfz command. It might be overkill, but that way you make sure that there are no files that have been changed by you or your configuration process.

Let us know how it goes