Step Six: Equilibration
Equilibration will be conducted much like in the case of a solvated protein. Generally a short NVT equilibration phase is followed by a longer NPT phase. The reason for this procedure is that we are now dealing with a heterogenous system, with both water and DPPC acting as solvent. Such heterogeneity requires a longer equilibration process. Water has to re-orient around the lipid headgroups and any exposed parts of the protein, and the lipids have to orient themselves around the protein as well. Such processes take some time, and lipid equilibration may take several ns of simulation time.
For membrane protein simulations, we will need to create special index groups consisting of solvent + ions and protein + lipids (explained below). To do this, use make_ndx:
gmx make_ndx -f em.gro -o index.ndx
At the make_ndx prompt, enter "16 | 14" to merge the SOL and CL groups. The new groups should be called "SOL_CL" by default.
Merge the Protein and DPPC groups by entering "1 | 13" at the make_ndx prompt. This group will be used for center-of-mass motion removal (more on this shortly).
We will once again start with NVT (with the script found here), calling grompp and mdrun just as we did at the EM step:
gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr gmx mdrun -deffnm nvt
Most of the parameters we are using are comparable to those in the lysozyme tutorial, with a few changes:
Again, use gmx energy to confirm that the temperature of the system has stabilized at 323 K before continuing. The choice of temperature should be based on the physical properties of the lipid, most notably the phase transition temperature. Some useful data that has been mined from the literature regarding area per lipid, phase transition temperatures, and/or parameter derivation for various lipids is presented here (see below). Please read the references and understand their implications. This list is not comprehensive; the references point to examples of literature wherein these particular lipids were used either for simulation or experimental work. The user should investigate further citations within these works, or subsequent papers that have cited these. The list should also not be viewed as comprehensive, as many other lipids have been successfully simulated. Presented here are some of the more common ones.
Having trouble with your system? Is it crashing during equilibration? Please see the Advanced Troubleshooting page.
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