GROMACS Tutorial

Step Three: Defining the Unit Cell & Adding Solvent

Now that you are familiar with the contents of the GROMACS topology, it is time to continue building our system. In this example, we are going to be simulating a simple aqueous system. It is possible to simulate proteins and other molecules in different solvents, provided that good parameters are available for all species involved.

There are two steps to defining the box and filling it with solvent:

  1. Define the box dimensions using the editconf module.
  2. Fill the box with water using the solvate module (formerly called genbox).

You are now presented with a choice as to how to treat the unit cell. For the purpose of this tutorial, we will use a simple cubic box as the unit cell. As you become more comfortable with periodic boundary conditions and box types, I highly recommend the rhombic dodecahedron, as its volume is ~71% of the cubic box of the same periodic distance, thus saving on the number of water molecules that need to be added to solvate the protein.

Let's define the box using editconf:

gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic

The above command centers the protein in the box (-c), and places it at least 1.0 nm from the box edge (-d 1.0). The box type is defined as a cube (-bt cubic). The distance to the edge of the box is an important parameter. Since we will be using periodic boundary conditions, we must satisfy the minimum image convention. That is, a protein should never see its periodic image, otherwise the forces calculated will be spurious. Specifying a solute-box distance of 1.0 nm will mean that there are at least 2.0 nm between any two periodic images of a protein. This distance will be sufficient for just about any cutoff scheme commonly used in simulations.

Now that we have defined a box, we can fill it with solvent (water). Solvation is accomplished using solvate:

gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p

The configuration of the protein (-cp) is contained in the output of the previous editconf step, and the configuration of the solvent (-cs) is part of the standard GROMACS installation. We are using spc216.gro, which is a generic equilibrated 3-point solvent model. You can use spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water, since they are all three-point water models. The output is called 1AKI_solv.gro, and we tell solvate the name of the topology file ( so it can be modified. Note the changes to the [ molecules ] directive of

[ molecules ]
; Compound  #mols
Protein_A       1 
SOL         10832 

What solvate has done is keep track of how many water molecules it has added, which it then writes to your topology to reflect the changes that have been made. Note that if you use any other (non-water) solvent, solvate will not make these changes to your topology! Its compatibility with updating water molecules is hard-coded.

Back: The Topology

Next: Adding Ions

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