CHARMM

CHARMM is a molecular simulation software from Harvard.

Install CHARMM

Requirements

gcc --version 

• Upgrade to at least GCC 7 ( if need) https://linuxhostsupport.com/blog/how-to-install-gcc-on-centos-7/

• Upgrade Cmake (version 3+)

Please make sure that you are using the same C and Fortran compiler version for these dependencies below otherwise CHARMM won’t compile

wget https://cmake.org/files/v3.20/cmake-3.20.5.tar.gz
tar xvzf cmake-3.20.5.tar.gz 
cd cmake-3.20.5/
make
make install
/usr/local/bin/cmake --version

Install OpenMPI https://mfix.netl.doe.gov/forum/t/openmpi-installation-in-centos7/543 Install OpenMM (It can be installed via conda, but it didn’t work for me. So I compiled from source code) Create conda environment and source http://docs.openmm.org/latest/userguide/library/02_compiling.html Install prerequisites conda install -c conda-forge cmake make cython swig fftw doxygen numpy Download the zip package here https://github.com/openmm/openmm/releases

cd /nfs/soft/openmm/
wget https://github.com/openmm/openmm/archive/refs/tags/7.7.0.zip
unzip 7.7.0.zip; mv openmm-7.7.0 install_7.7.0
cd install_7.7.0
mkdir build; cd build
cmake -D CMAKE_INSTALL_PREFIX=/nfs/soft/openmm/openmm-7.7.0.3/ -D OPENCL_LIBRARY=/nfs/soft/cuda-10.0/lib64/libOpenCL.so ..
make -j 10
make install

Compile CHARMM

cd /nfs/soft/CHARMM/charmm

Download the package, ask Yujin

tar xf c47b1.tar
cd charmm
mkdir build; cd build

Source the conda environment above conda install -c conda-forge fftw

export FFTW_HOME="/nfs/soft/anaconda3/pkgs/fftw-3.3.10-nompi_ha7695d1_103"; export CUDA_BIN_PATH="/nfs/soft/cuda-10.0/bin"; 

export OPENMM_HOME="/nfs/soft/openmm/openmm-7.7.0.3/";

../configure  -D MPI_Fortran_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpifort  -D MPI_C_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpicc   --with-gcc -u --with-fftdock --with-blade --without-mkl --with-openmm -p ../install_blade2

make -j 10
make install