MD Simulations

This repository contains all the necessary information for running MD Simulations

Installation of GROMACS

Here are the codes which can be given one after the other to install the latext version of GROMACS on any computer. The link to the related video is at the following link:

https://www.youtube.com/watch?v=kA3SmMnphmI

First of all open the terminal and issue the following command to update the system.

sudo apt-get update

After the completion of update, issue following command:

sudo apt-get upgrade

Now, we have to check that whether we have already installed cmake in our system. For this, we will check the version of the cmake.

cmake -version

Next, if we cannot see the version of cmake, then issue following command to install it.

sudo apt-get install cmake

Now, some other libraries for building the package are also required, which can be installed using this command in the terminal. Press Y when will be required.

sudo apt-get install swig
sudo apt-get install libboost-all-dev
sudo apt-get install cmake-data
sudo apt-get install liblog4cpp5-dev
sudo apt-get install libitpp-dev
sudo apt-get install libcppunit-dev
sudo apt-get install gnuradio-dev
sudo apt-get install build-essential

Now go to the Downloads folder. The following command will only work if you are in home.

cd Downloads/

Make a new directory over there in Downloads folder and name it GromacsDownload.

mkdir GromacsDownload

Change directory to GromacsDownload by issuing the following command.

cd GromacsDownload/

In this directory, you have to download two files from http://manual.gromacs.org/documentation/2020/download.html. For this, we can use wget.

wget http://gerrit.gromacs.org/download/regressiontests-2020.tar.gz
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz

Now we will issue following commands one by one to unzip/untar the compressed downloaded files in the same direcotry.

tar xvzf regressiontests-2020.tar.gz
tar xvzf gromacs-2020.tar.gz

After this, we have to install the FFTW on our system.

sudo apt-get install libfftw3-dev

Now, change your directory to gromacs-2020 which was earlier uncompressed.

cd gromacs-2020/

Here, we will make a new directory with the name build.

mkdir build

change your directory to build.

cd build/

Now, issue the following command. DREGRESSIONTEST_DOWNLOAD is turned OFF because we have downloaded it manually and will perform the regression tests using the dedicated path to that folder of regression tests downloaded earlier.

DGMX_BUILD_OWN_FFTW is turned OFF because we have installed it separately by using:

sudo apt-get install libfftw3-dev in that video.

If you turned these flags ON then you do not need to do these manually. The answers are given in this Gromacs manual.

http://manual.gromacs.org/documentation/5.1/install-guide/index.html

sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=gcc -DREGRESSIONTEST_PATH=/home/rehan/Downloads/GromacsDownload/regressiontests-2020

Now issue this command.

sudo make check

Now install the gromacs using following command.

sudo make install

You have finally installed GROMACS, issue following command to source it. Without this command, you cannot call gmx directly in the terminal easily. Moreover, you want to use gromacs any time after restrating your computer. Please issue the same command before using gmx, otherwise, gmx will not be available.

source /usr/local/gromacs/bin/GMXRC

You can check the version and installation of gromacs by issuing the following command.

gmx pdb2gmx --version

Note: Clerical mistakes are expected. Please suggest any changes in this document.