GROMACS has been a most used Molecular dynamics simulation engine in the last couple of years. Thanks to the increasing power of computer. When I staret doing simnulation GROMACS was installe on our computing cluster and I had started right way to do the simulation. Later when I need to used some recent version of it, I was perplexed. I have included here how to install GROMACS so we can make most of it and patch GROMACS with PLUMED. PLUMED is a PLUmed MolEcular Dynamics simulation package which is very useful in estimating free energy. It has both Umbrella Sampling and Metadynamics techniques. All this installation tutorial is intended for HPC but it also works for a personal machine too
- gcc compiler
- fftw
- OpenMPI (for parallelization)
- cmake
I prefer to download all the software and compiler in the source folder. Download the gcc compiler directly to your machine
wget http://mirror.rit.edu/gnu/gcc/gcc-8.5.0/gcc-8.5.0.tar.gz
Extract the files
tar -xvf gcc-8.5.0/gcc-8.5.0.tar.gz
Go to gcc-8.5.0 folder
cd gcc-8.5.0
Download all the prerequisite for gcc to compile
sh contrib/download_prerequisites
make a new directory inside gcc-8.5.0 and go to that folder
mkdir build
cd build
Configure
../configure --prefix=/lscratch/apps/gcc/8.5.0 --enable-languages=c,c++,fortran,go --disable-multilib
Compile (this will take a little while ~20 mins
make- j 10 bootstrap
Install
make install
CONGRATULATIONS!!! gcc is now installed
If you are working in a HPC it is always helpful to make a modulefiles for all the software that you installed. Lets make a module file for gcc. Make a folder called modulesfiles in your home directory and make a gcc folder inside modulefiles
mkdir modulefiles
cd modulefiles
mkdir gcc
Make module files with in it. I named this module file according to version of the software because it will be easier if I have to installed the updated one again.
touch 8.5.0
paste this lines to the 8.5.0 file
#%Module1.0
set root_dir /lscratch/apps/gcc/8.5.0
prepend-path LD_LIBRARY_PATH $root_dir/lib:$root_dir/lib64
prepend-path MANPATH $root_dir/share/man
prepend-path PATH $root_dir/bin
prepend-path CMAKE_PREFIX_PATH $root_dir
setenv CC gcc
setenv CXX g++
setenv FC gfortran
setenv F77 gfortran
setenv F90 gfortran
setenv F95 gfortran
NOTE: To specify a default module within a modulefiles folder (In case if you have multiple version) , create a file called .version and paste the lines below
#%Module1.0#
set ModulesVersion "gcc-8.5.0"
Now you can import the gcc compiler in you machine
module load gcc-8.5.0
Now install FFTW, will come back later and complete it.