Downlaod VMD from the software download page here

Extract the vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz file to vmd-1.9.3 and change directory.

$ cd /path/to/file/vmd-1.9.3

Run configure to see list of options available

$ ./configure

Run configure to select the options

$ ./configure LINUXAMD64 OPENGL TK CUDA TCL PYTHON NUMPY

Change directory to src

$ cd src

Install

$ sudo make install

$ sudo apt install gcc

tar xzvf cmake-3.12.2.tar.gz

cd cmake-3.12.2/

./bootstrap

make -j 4

sudo make install

Verify the GPU is CUDA capable

$ lspci | grep -i nvidia

Check if the Ubuntu version is supported by CUDA toolkit

$ uname -m && cat /etc/*release

Check the GCC version currently installed

$ gcc --version

Check the kernel version

$ uname -r

Install kernel headers

$ sudo apt-get install linux-headers-$(uname -r)

Download the base installer from NVIDIA download page and install

Linux _ x86_64 _ Ubuntu _ 18.04 _  deb(network) 

$ sudo dpkg -i cuda-repo-ubuntu1804_10.0.130-1_amd64.deb

Install CUDA repository GPG key

$ sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub

Update

sudo apt-get update

Install CUDA

$ sudo apt-get install cuda

To permanently add CUDA to the path

$ vi ~/.bashrc

Add path:

export PATH=/usr/local/cuda-10.0/bin:PATH

export LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:$LD_LIBRARY_PATH

Check installation by entering in terminal

$ nvcc -V

$ cat /proc/driver/nvidia/version

Reboot

Test

$ cp  -r /usr/local/cuda-10.0/samples/ ./

$ cd samples/1_Utilities/deviceQuery/

$ make

$ ./deviceQuery

Result should be PASS

After installing required softwares such as gcc compiler, cmake, fftw and optional packages like CUDA, MPI, etc.

Download GROMACS package from official site

Extract the contents of downloaded file

cd gromacs-2016.4/

mkdir build

cd build/

cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-10.0/ -DGMX_BUILD_OWN_FFTW=ON _DREGRESSIONTEST_DOWNLOAD=ON _DCMAKE_INSTALL_PREFIX=/usr/local/gromacs16

make -j 4

sudo make install

export PATH=/usr/local/gromacs16/bin:$PATH

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs20 -DREGRESSIONTEST_PATH=/home/raviteja/Downloads/regressiontests-2020