GROMACS Tutorial

Step Five: Energy Minimization

Now that the system is assembled, create the binary input using grompp using this input parameter file:

gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr

Note that in this .mdp file, I have set energygrps = Protein JZ4. It may be of interest to examine the various components of the nonbonded interactions between your protein and ligand. This is a good practice in case anything goes wrong.

Make sure you have been updating your topol.top file when running genbox and genion, or else you will get lots of nasty error messages ("number of coordinates in coordinate file does not match topology," etc).

We are now ready to invoke mdrun to carry out the EM:

gmx mdrun -v -deffnm em

For me, the system converged relatively quickly:

Steepest Descents converged to Fmax < 1000 in 178 steps
Potential Energy  = -5.0933919e+05
Maximum force     =  9.1495343e+02 on atom 1266
Norm of force     =  5.1248310e+01

As in the lysozyme tutorial, it is possible to monitor various components of the potential energy using the energy module. I will not illustrate these principles here. Have fun.

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

Back: Add Ions Next: Equilibration

Bevan Lab Homepage

Virginia Tech Homepage

Virginia Tech Biochemistry


Site design and content copyright 2008-2015 by Justin Lemkul
Problems with the site? Send them to the Webmaster