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 .
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.
*.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 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 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
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
The final frame of minimization (the structure in
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
integrator = l-bfgs) minimizer.
For details, see Run control options in the MDP file.