Software

Build and install GROMACS

1. Get the code from GROMACS web page:

   wget https://ftp.gromacs.org/gromacs/gromacs-2022.5.tar.gz
   tar -xvf gromacs-2022.5.tar.gz
   cd gromacs-2022.5
   

Alternatively, you can checkout required version using Git:

git clone https://gitlab.com/gromacs/gromacs.git
cd gromacs
git checkout v2022.5

2. Build and install

   mkdir build
   cmake -S. -Bbuild
   cd build
   make -j4
   sudo make install
   

Optionally, one can set the installation path by adding -DCMAKE_INSTALL_PREFIX=/your/desired/path to the cmake command.

3. You can optionally check the build before installing by running the tests:

   make check -j4
   

4. It is convenient to set a variable for GROMACS executable. If you install into the default location:

   GMX=/usr/local/gromacs/bin/gmx
   

Force-fields

TraPPE-UA

Get the forcefield files:

git clone https://github.com/wesbarnett/trappeua.git

gmx pdb2gmx utility uses enumeration for the water model selection. Hence, one need the water mode to have one of the pre-defined names, which is not the case in the trappeua implementation we just downloaded. In order to use pdb2gmx later on, we now need to rename the water model file for tip4p model and change this name in the watermodels.dat file before we copy forcefield to the GROMACS installation folder:

mv trappeua/trappeua.ff/tip4p2005.itp trappeua/trappeua.ff/tip4p.itp
sed -i 's/tip4p2005/tip4p/' trappeua/trappeua.ff/watermodels.dat

To install the forcefield, copy the result to GROMACS installation folder. Assuming that GROMACS in installed at /usr/local/gromacs:

sudo cp -pr trappeua/trappeua.ff /usr/local/gromacs/share/gromacs/top/

Note that you can also keep force-field files in your local folder without installing.

CHARMM36

Download and extract the force-field files:

wget http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2022.ff.tgz
tar -xvf charmm36-jul2022.ff.tgz

Or clone this repository:

git clone git@gitlab.com:artemzhmurov/charmm36.git

To install the forcefield, copy it to your GROMACS installation folder. Assuming that GROMACS in installed at /usr/local/gromacs:

sudo cp -pr trappeua/charmm36.ff /usr/local/gromacs/share/gromacs/top/

Note that you can also keep force-field files in your local folder without installing.

PackMol

To create the coordinates for a box of molecules, we can use Packmol software. You will need gfortran, which you can install by running sudo apt install gfortran. To get and install Packmol:

git clone https://github.com/m3g/packmol.git
cd packmol
git checkout v20.3.5
./configure
make
PACKMOL=$(pwd)/packmol

VMD

Visual Molecular Dynamics (VMD) is a visualization program, that should be installed locally. You can get a copy here.