What is OpenMD?

OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. “sticky” atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat interfaces, and nanoparticles) have all been simulated using force fields included with the code. OpenMD works on parallel computers using the Message Passing Interface (MPI), and comes with a number of analysis and utility programs that are easy to use and modify. An OpenMD simulation is specified using a very simple meta-data language that is easy to learn.

OpenMD lab (examples, etc.)

We will install the OpenMD 2.6 version

Prerequisities

For Opensuse

fftw
fftw-devel
cmake
openbabel
openbabel-devel
openmpi3
openmpi3-devel
perl
python3-numpy
python3-scipy
qhull
qhull-devel
zlib
zlib-devel


For Ubuntu

libfftw3-3
libfftw3-dev
cmake
openbabel
libopenbabel-dev
openmpi-bin
libopenmpi-dev
perl
python3-numpy
python3-scipy
qhull-bin
libqhull-dev
minizip
zlib1g-dev


Downloading

curl -o openmd-2.6.tar.gz http://openmd.org/releases/openmd-2.6.tar.gz


Installing

* untar and change to it

tar zxf openmd-2.6.tar.gz
cd openmd-2.6


* create build directory and change to it 

mkdir build
cd build

* configure 

cmake ../


* compile

make

or 

make -j4  # for 4 processors


* install

umask 0022; sudo make install

 

*Add the path to the  ~/.bashrc   file 

kwrite ~/.bashrc

add the following lines and modify the path according to your case

#----openMD path-----------------
export OMDROOT=/home/algerien/abinitio/openmd-2.6/build/bin
export PATH=$PATH:$OMDROOT
#-----------------------------------

 * Source the file

source ~/.bashrc

 

Reference: https://openmd.org/building-and-installing-openmd-2/