First Molecular Dynamic Simulation
Step-4. Adding Ions

Pietro Buffa

The Gromacs tool for adding ions is called genion. This program simply reads the topology file and replace water molecules with the ions that the user specifies. Before using genion, we need to generate an important file which has a .tpr extension. This file is produced by the Gromacs tool grompp (gromacs pre-processor) and includes all the parameters for all the atoms in the system. To this end, we also need an additional imput file with .mdp extension (molecular dynamics parameter file) in order to specify all the parameters. A .mdp file is normally used to run energy minimization or a MD simulation but, in this case, it is simply used to generate an atomic description of the entire system. You can download [here] the .mdp file that we are going to use and save it into your work directory.

Now, we are ready to assemble a .tpr file using the following command:

> grompp -f ions.mdp -c 1AKI-solv.gro -p topol.top -o ions.tpr

...and we will finaly pass this file to genion using the following command:

> genion -s ions.tpr -o 1AKI-solv-ions.gro -p topol.top -pname NA+ -nname CL- -nn 8 -random -rmin 1.0

When prompted, choose group 12 "SOL" for embedding ions.

We are asking genion to generate a file of the entire system (1AKI-solv-ions.gro), which include the correct number of ions necessary to neutralize the net charge of the protein (+8e, if you remember). In this case, we are adding 8 negative ions CL- (-nn 8) but of course, you can have specific cases where you have to add x positive ions like Na+ (-np x).

Take a look at the end of the file topol.top because you will find some new lines:

SOL = number of water molecules added to the system
NA+ = number of positive ions added to the system
CL- = number of negative ions added to the system

In this case, we don't have any NA+ molecule so, you have to delete this line from the file using an editor and save it because previous version of Gromacs could generate an error.

If until this point everything is alright, you should visualize your system simply passing the "1AKI-solv-ions.gro" to a graphical visualizer like VMD.

Go to the Step-5.

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