GROMACS
-------------
https://www.gromacs.org/

- Download
	https://manual.gromacs.org/2023.2/download.html
- Installation
	https://manual.gromacs.org/2023.2/install-guide/index.html
	
	I went with full istallation because I will need that on JICluster 
	but NOT with the 'Note' right below.  
	
	Note: If you have ubuntu, installing gromacs to just play with it is easily done with entering apt install gromacs at a command line, though this will not give you the highest performance, it gives you something to start.
	
	
	==============		
	Get the latest version of your C and C++ compilers:
	https://www.cyberithub.com/how-to-update-or-upgrade-gcc-to-latest-version-on-ubuntu-debian/	
	- sudo apt update && sudo apt upgrade
	- sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test 
	- sudo apt update
	- sudo apt install gcc-11
	- sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 20  -> already latest, skipped  
	- gcc --version
	
	Check that you have CMake version 3.18.4 or later.
	- cmake --version
		
	tar xfz gromacs-2023.2.tar.gz
	cd gromacs-2023.2
	mkdir build
	cd build
	cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON  
	make
	make check
	sudo make install		(or mkdir GROMACS; make DESTDIR=/home/mabovsky/Local/gromacs install) 	
	source /usr/local/gromacs/bin/GMXRC	(or source /home/mabovsky/Local/gromacs/bin/GMXRC)
	
	
	
	
			=========== (ijcluster / mabovsky / Local) ==============

	
	cmake --version  ->  no cmake
	(download cmake) -> https://cmake.org/download/  ->  cmake-3.26.5-linux-x86_64.tar.gz
	(install cmake)  -> https://askubuntu.com/questions/1053329/installing-cmakes-latest-version-from-binary-without-using-sudo
	cd /home/mabovsky/Local
	tar xvf cmake-3.26.5.tar.gz
	cd cmake-3.26.5 
	./bootstrap --prefix=$HOME/Local/cmake
	make
	make install
	cd .. 
	cd cmake
	cd bin
	/home/mabovsky/Local/cmake/bin/cmake --version
	cd /home/mabovsky/Local
	rm -r cmake-3.26.5
	/home/mabovsky/Local/cmake/bin/cmake --version
	
	
	(gcc)	
	conda install -c conda-forge cxx-compiler 	-> gcc (Anaconda gcc) 11.2.0
	
	
	
	(gromacs) -> https://manual.gromacs.org/5.1.2/install-guide/index.html
	cd /home/mabovsky/Local
	tar xvf gromacs-2023.2.tar.gz
	cd gromacs-2023.2
	mkdir build
	cd build
	/home/mabovsky/Local/cmake/bin/cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=$HOME/Local/gromacs -DGMX_FFT_LIBRARY=fftpack
	make
	make check
	make install
	

	
	
				========  (ijcluster / mabovsky / Local2)  =========
	
	 -> https://www.fftw.org/ 
	(download  fftw-3.3.10.tar.gz) -> https://www.fftw.org/download.html
	(installation) -> https://www.fftw.org/doc/Installation-on-Unix.html
	tar xvf fftw-3.3.10.tar.gz
	cd fftw-3.3.10
	-- bad -> ./configure --enable-shared --enable-float --enable-openmp --enable-sse --enable-sse2 --enable-avx --enable-avx2 --prefix=/home/mabovsky/Local2/fftw3
	./configure --enable-float --enable-openmp --enable-sse --enable-sse2 --enable-avx --enable-avx2 --prefix=/home/mabovsky/Local2/fftw3
	make
	make check
	make install

	
	(help) -> https://manual.gromacs.org/current/dev-manual/build-system.html
	
	(downloaded from) -> https://manual.gromacs.org/2023.3/download.html
	cd /home/mabovsky/Local2
	tar xvf gromacs-2023.3.tar.gz
	cd gromacs-2023.3
	mkdir build
	cd build
	/home/mabovsky/Local/cmake/bin/cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_PREFIX_PATH=/home/mabovsky/Local2/fftw3 -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_SHARED_EXE=OFF -DCMAKE_INSTALL_PREFIX=$HOME/Local2/gromacs 
	make
	make check	//  < 6 min
	make install
	

	
	
			========  (ijcluster / mabovsky / Local3 with MPI support)  =========
	
	-- (mpicxx) // https://anaconda.org/conda-forge/openmpi-mpicxx
	-- conda install -c conda-forge openmpi-mpicxx 	-> mpicxx compiler
	
	// Install OpenMPI
	https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf	 
	https://www.open-mpi.org/software/ompi/v5.0/ 	->  openmpi-5.0.0.tar.gz	
	tar xvf openmpi-5.0.0.tar.gz
	cd openmpi-5.0.0 
	./configure --prefix=/home/mabovsky/Local3/openmpi
	make -j10 all		// use 10 core to compile
	make install
	
	Something wrong!!! mpicxx --version still show g++ version!!! 
	
	Resume: Because, I am not able to compile gromacs-mpi, I will move to NAMD.
	2023-11-30.	
	
	
	
	
	
- GROMACS Tutorial: Molecular Dynamics simulation of a protein in water environment
https://www.compchems.com/gromacs-tutorial-molecular-dynamics-simulation-of-a-protein-in-water-environment/#background-for-molecular-simulation


- How to run a Molecular Dynamics simulation using GROMACS
https://www.compchems.com/how-to-run-a-molecular-dynamics-simulation-using-gromacs/


- Molecular Dynamics (MD)
https://www.compchems.com/categories/molecular-dynamics-md/


- How can I do simulation of a protein-protein complex in Gromacs?
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https://www.researchgate.net/post/How_can_I_do_simulation_of_a_protein-protein_complex_in_Gromacs