3. Energy minimization

In order to remove “clashes” (i.e. close overlaps of the LJ cores) we perform an energy minimization: Instead of a MD simulation we use an algorithm to change the coordinates in such a way as to reduce the total potential energy.

3.1. Set up and generate the run file

First, we will copy a file from the templates folder (provided in this tutorial) that tells Gromacs MD program how to do energy minimization:

cp ../templates/em.mdp .

Tip

Have a look at the MDP file to get a feel for what kinds of settings can be adjusted to suit one’s needs. Individual parameters are explained in more detail in mdp options.

The *.mdp file contains the settings that dictate the nature of the simulation. For energy minimization, we will use the simple steepest descent minimizer (integrator = steep in em.mdp, which runs in parallel). Use gmx grompp (the GROMacs PreProcessor) to generate the run input file (TPR) from the run parameter file (MDP), coordinate file (the solvated system with ions; PDB), and the topology (TOP):

cd ../emin
gmx grompp -f em.mdp -c ../solvation/ionized.pdb -p ../top/4ake.top -o em.tpr

3.2. Perform energy minimization

The energy minimization is performed with gmx mdrun but by using the appropriate integrator option in the Run control options in the MDP file it has been instructed to do a energy minimization:

gmx mdrun -v -s em.tpr -deffnm em -c em.pdb

Ideally, the maximum force Fmax (gradient of the potential) should be < 1e+03 kJ mol^-1 nm^-2 (but typically anything below 1e+05 kJ mol^-1 nm^-2 works). See the screen output or the em.log file for this information.

Tip

The final frame of minimization (the structure in em.pdb) can be used as the input structure for further minimization runs. It is common to do an initial energy minimization using the efficient steepest descent method and further minimization with a more sophisticated method such as the conjugate gradient algorithm (integrator = cg) or the Newton-like Broyden-Fletcher-Goldfarb-Shanno (integrator = l-bfgs) minimizer. For details, see Run control options in the MDP file.