In order to remove “clashes” (i.e. close overlaps of the LJ cores) we perform an energy minization: Instead of a MD simulation we use an algorithm to change the coordinates in such a way as to reduce the total potential energy.
We 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):
grompp -f em.mdp -c ../solvation/ionized.pdb -p ../top/4ake.top -o em.tpr
Note
The MDP file em.mdp is provided in templates/em.mdp: copy it to the emin/ directory. You should have a look at it and modify it according to your needs. The individual parameters are explained under mdp options.
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 minimization:
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.
If you want to minimize further, you can use the :file”em.pdb structure as an input for a second run with either the conjugate gradients (integrator = cg) or the Newton-like Broyden-Fletcher-Goldfarb-Shanno (integrator = l-bfgs) minimizer. For details see Run control options in the MDP file.