Adding a Protein to the Aqueous Layer

Interested in how a protein or peptide might interact with such a biphasic system? The same principles as before apply to positioning the protein: place the protein in the unit cell of desired dimensions, and manually set its center. For our system, we can assign a generic peptide to a position in the "top" half of the box with editconf like so:

gmx editconf -f peptide.gro -o peptide_newbox.gro -box 4.30795 4.30795 8.6159 -center 2.153975 2.153975 6.461925

The assigned z-position for the protein center is three-quarters of the box length (original cyclohexane box plus one-half).

How do we place that protein in the same unit cell as our cyclohexane layer? We could use the Unix comand cat, but then there's internal cleanup to do (removal of unnecessary lines, counting numbers of atoms, etc). All of that is pretty easy, but why do several steps when we can just do one? What we can do is actually use chx_newbox.gro as a solvent. It has the same dimensions as the box in which we have positioned our fictional peptide, so it should assemble quite nicely:

gmx solvate -cp peptide_newbox.gro -cs chx_newbox.gro -o peptide_chx.gro

Using the KALP₁₅ peptide from the membrane protein tutorial, the system would look something like this:

Then proceed with another round of solvate to add water, as before. Energy-minimize, equilibrate, and simulate.

Expanding the Box

Let's say your protein is too large for a box that is only ~4.3 nm in the x-y plane. It is possible to expand your system simply by using genconf:

gmx genconf -f chx_10ns.gro -nbox 2 2 2 -o chx_bigbox.gro

The above command will create a new, 8.6-nm cube of cyclohexane with 8 times the number of molecules in it. Again, it is not necessary to create a cube. Then follow all the steps outlined previously for positioning this new, larger layer in a box, adding whatever protein or solute you desire, and filling the box with water.

In lieu of a new, cubic box, an expanded layer can be created along the x-y plane with a slightly different command:

gmx genconf -f chx_10ns.gro -nbox 2 2 1 -o chx_biglayer.gro

Summary

You have now built a biphasic cyclohexane-water system, and hopefully understand the basic principles of how to place any arbitrary molecule into such a system in a desired location.

If you have suggestions for improving this tutorial, if you notice a mistake, or if anything is otherwise unclear, please feel free to email me. Please note: this is not an invitation to email me for GROMACS problems. I do not advertise myself as a private tutor or personal help service. That's what the GROMACS User Forum is for. I may help you there, but only in the context of providing service to the community as a whole, not just the end user.

Happy simulating!