# System preparation¶

There are many ways to prepare a simulation system to run with GROMACS. These often vary with the kind of scientific question being considered, or the model physics involved. A protein-ligand atomistic free-energy simulation might need a multi-state topology, while a coarse-grained simulation might need to manage defaults that suit systems with higher density.

## Steps to consider¶

The following general guidance should help with planning successful simulations. Some stages are optional for some kinds of simulations.

1. Clearly identify the property or phenomena of interest to be studied by performing the simulation. Do not continue further until you are clear on this! Do not run your simulation and then seek to work out how to use it to test your hypothesis, because it may be unsuitable, or the required information was not saved.
2. Select the appropriate tools to be able to perform the simulation and observe the property or phenomena of interest. It is important to read and familiarize yourself with publications by other researchers on similar systems. Choices of tools include:
• software with which to perform the simulation (consideration of force field may influence this decision)
• the force field, which describes how the particles within the system interact with each other. Select one that is appropriate for the system being studied and the property or phenomena of interest. This is a very important and non-trivial step! Consider now how you will analyze your simulation data to make your observations.
3. Obtain or generate the initial coordinate file for each molecule to be placed within the system. Many different software packages are able to build molecular structures and assemble them into suitable configurations.
4. Generate the raw starting structure for the system by placing the molecules within the coordinate file as appropriate. Molecules may be specifically placed or arranged randomly. Several non-GROMACS tools are useful here; within GROMACS gmx solvate, gmx insert-molecules and gmx genconf solve frequent problems.
5. Obtain or generate the topology file for the system, using (for example) gmx pdb2gmx, gmx x2top, SwissParam (for CHARMM forcefield), PRODRG (for GROMOS96 43A1), Automated Topology Builder (for GROMOS96 53A6), MKTOP (for OPLS/AA) or your favourite text editor in concert with chapter 5 of the GROMACS Reference Manual. For the AMBER force fields, antechamber or acpype might be appropriate.
6. Describe a simulation box (e.g. using gmx editconf) whose size is appropriate for the eventual density you would like, fill it with solvent (e.g. using gmx solvate), and add any counter-ions needed to neutralize the system (e.g. using gmx grompp and gmx insert-molecules). In these steps you may need to edit your topology file to stay current with your coordinate file.
7. Run an energy minimization on the system (using gmx grompp and gmx mdrun). This is required to sort out any bad starting structures caused during generation of the system, which may cause the production simulation to crash. It may be necessary also to minimize your solute structure in vacuo before introducing solvent molecules (or your lipid bilayer or whatever else). You should consider using flexible water models and not using bond constraints or frozen groups. The use of position restraints and/or distance restraints should be evaluated carefully.
8. Select the appropriate simulation parameters for the equilibration simulation (defined in mdp file). You need to choose simulation parameters that are consistent with how force field was derived. You may need to simulate at NVT with position restraints on your solvent and/or solute to get the temperature almost right, then relax to NPT to fix the density (which should be done with Berendsen until after the density is stabilized, before a further switch to a barostat that produces the correct ensemble), then move further (if needed) to reach your production simulation ensemble (e.g. NVT, NVE). If you have problems here with the system blowing up, consider using the suggestions on that page, e.g. position restraints on solutes, or not using bond constraints, or using smaller integration timesteps, or several gentler heating stage(s).
9. Run the equilibration simulation for sufficient time so that the system relaxes sufficiently in the target ensemble to allow the production run to be commenced (using gmx grompp and gmx mdrun, then gmx energy and trajectory visualization tools).
10. Select the appropriate simulation parameters for the production simulation (defined in mdp file). In particular, be careful not to re-generate the velocities. You still need to be consistent with how the force field was derived and how to measure the property or phenomena of interest.

## Tips and tricks¶

### Database files¶

The share/top directory of a GROMACS installation contains numerous plain-text helper files with the .dat file extension. Some of the command-line tools (see Command-line reference) refer to these, and each tool documents which files it uses, and how they are used.

If you need to modify these files (e.g. to introduce new atom types with VDW radii into vdwradii.dat), you can copy the file from your installation directory into your working directory, and the GROMACS tools will automatically load the copy from your working directory rather than the standard one. To suppress all the standard definitions, use an empty file in the working directory.