GROMACS Tutorial

Step Five: Energy Minimization

This step is just like in any other simulation. Assemble the binary input using grompp using this input parameter file:

gmx grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr

Invoke mdrun:

gmx mdrun -v -deffnm em

As with any other simulation, verify that the values of Epot and Fmax are reasonable before continuing. Membrane protein systems can be tricky, because there are a number of potential problems. If your system is not converging, consider the following factors:

  1. Intra-headgroup hydrogen bonding, like in PE or PG headgroups. Sometimes simulations collapse because the headgroups fold in on themselves within voids in the solvent. There are several potential solutions to this problem (and others you may encounter):
    • Use position restraints or freeze groups during equilibration until the solvent is optimized around the lipid headgroups.
    • Reduce the charges on the H atoms (all the way to zero, if necessary) Restore the charges before continuing!
    • Add [ exclusions ] within the topology between H and phosphate O atoms Remove the exclusions before continuing!
  2. Acyl chain overlap can occur during packing. Run InflateGRO carefully, and do not attempt to over-pack your lipids.
  3. Protein-lipid overlap. Did you choose an appropriate cut-off value in the initial InflateGRO step?
  4. Water-headgroup and ion-headgroup overlap. Sometimes genbox and genion are not smart, especially regarding random placement of ions. A CL- next to a phosphate can send the ion (or lipid) careening across the simulation box!

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

Back: Add Ions

Next: Equilibration


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