First Molecular Dynamic Simulation
Step-3. Defining a Box and Adding Solvent

Pietro Buffa

We are going to simulate a simple aqueous system. First of all we need to define a specific box in which you want to put your protein and to fill it with solvent. To this end, we can use other two important gromacs tools:

editconf = it defines the box dimensions
genbox = it fills the box with water

In this tutorial we will use a simple cubic box as the unit cell, using the following command:

> 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 because we must satisfy the minimum image convention. The protein should never see its periodic image otherwise the forces calculated will be spurious. A solute-box distance of 1.0 nm means that we have at least 2.0 nm between any two periodic images of the protein.

Now that we have defined a box, we can fill it with solvent (water) using the following command:

> genbox -cp 1AKI-newbox.gro -cs spc216.gro -o 1AKI-solv.gro -p topol.top

The configuration of the protein (-cp) is conteined in the output of the previous step while, 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. We will call the output file (1AKI-solv.gro) and we have to pass to the program the topology file so it can be modified.

Go to the Step-4.

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