Energy Minimization

During the setup of our system we might have introduced unnatural stress, for example by placing two atoms accitentally too close to each other. This might result in large forces acting on the particles that would blow up our system should we simply start a regular molecular dynamics simulation at this point. To cope with this problem we will perform an energy minimization in which we relax the system to the closest local energy minimum. We will again first generate a run-input or .tpr file with grompp to combine the initial setup with the algorithms and parameters from an .mdp file:

gmx grompp -f em.mdp -po em.out.mdp -c kigaki_ions.gro -p -o em.tpr

The result is a .tpr file that is the only file needed to start our energy minimization. Some new parameters are introduced in the file em.mdp. Examine it and also have a look again at the mdp section of the Gromacs Online Reference to familiarize with all the parameters.
We now use a steepest descent algorithm to locate the closest local minimum and set some convergence criteria. In addition we set the coordinate output frequency to every 10 steps with nstxout = 10. The energy minimization can be run with:

gmx mdrun -v -deffnm em

The -v switch will make mdrun create verbose output and report the computation progress. -deffnm defines a default filename prefix that is used for all in- and output files. The corresponding file endings will be appended for the different in- and output files, so they do not need to be specified each individually. You will obtain a number of output files. The file em.log contains detailed information on several energy terms throughout the simulation and a performance analysis at the end. The file em.gro contains the coordinates of the final configuration of the system. The file em.trr contains coordinates (and optionally velocities in case of MD) and forces for each output frame. The em.edr file contains information on different energy terms and, if applicable for the simulation, information on the temperature, pressure, volume and some other quantities during the simulation. You can extract this information with:

gmx energy -f em.edr -o em_Epot.xvg

Follow the instructions to select the potential energy. You can plot the graph with the program xmgrace:

xmgrace em_Epot.xvg

You should see a monotonically decaying graph as the potential energy gets minimized. You can also follow the equilibration process with VMD. It is a good idea to ensure that all molecules are complete in the simulation box and do not cross the periodic boundaries to stick out on one end and enter again on the opposite. This would give a huge mess in VMD. You can transform the trajectory with:

gmx trjconv -f em.trr -s em.tpr -o em_centered.xtc -ur compact -pbc mol -center

Select the protein group for centering and the whole system for output. The trajectory will be converted into another file format (*.xtc) that has less precision, but is much tighter compressed, resulting in smaller files. Now load the system into VMD with:

vmd em.gro

This will load the final configuration stored in em.gro. The information on bonds are automatically generated by VMD. You can optionally delete the coordinates by right clicking on the molecule in the main window and deleteing the single frame. This will make the molecule dissapear in the display window, but the information on atom types and bonds is still retained internally in VMD. This has the advantage that we will not see a jump from the final configuration (as loaded from em.gro) to the first frame of the trajectory. The trajectory can be loaded by selecting File -> New Molecule from the VMD main window. First select the already loaded molecule from the drop down menu. Then browse to the trajectory file em_centered.xtc. The filetype will be detected automatically. Hit the load button.