First Molecular Dynamic Simulation
Step-5. Energy Minimization

Pietro Buffa

The our solvated and electroneutral system has been prepared but, we are not ready to start dynamic simulation yet. We have to be sure that 1) our initial structure doesn't have any inappropriate internal geometry 2) the solvation process has not introduced some bad contacts. We can solve all these problems through a process called Energy Minimization (EM). EM is used to find a local energy minimum near the starting system in order to relax it. There are three energy minimization methods currently implemented in Gromacs:

* Steepest Descents
* Conjugate Gradient

The process is quite similar to previous one, we are going to use grompp to assemble structure, topology and simulation parameters into a binary file .tpr but, this time, we will run energy minimization using the Gromacs MD engine: mdrun. Download [here] the .mdp file that we are going to use, save it into your work directory and run the following two commands:

> grompp -f minim.mdp -c 1AKI-solv-ions.gro -p topol.top -o em.tpr

> mdrun -v -s em.tpr -o em.trr -e em.edr -c em.gro -g em.log

The mdrun tool will take the file "em.tpr" in input and it will generate four different files:

em.trr (Binary file for trajectory)
em.edr (Binary energy file)
em.gro (Energy-minimized structure)
em.log (ASCII-text log file for EM process)

Now, we have to pay attention to two different things which can be noticed at the end of this process. The Potential Energy (Epot) which has to be negative and the Maximum Force (Fmax) which has to be no greater than the value setted into the file "minim.mdp", in our case "emtol = 1000.0" indicating a target Fmax no greater than 1000.0 kJ/mol/nm.

The "em.edr" file contains all the energy terms that Gromacs collects during EM process. We can analyze any .edr file using the following Gromacs tool:

> g_energy -f em.edr -o potential.xvg

At the prompt type "10 0" to select Potential (10) and to finish (0). If you want to have a graphical presentation of these data, you need "xmgrace plotting tool". If this program has already installed on your computer, you can simply type the following command and it will show you the nice steady convergence of Epot:

> xmgrace potential.xvg

Now that our system is at an energy minimum, we can begin the real dynamics.

Go to the Step-6.

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