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GROMACS Wizard - Coarse-grained systems#

This section is a part of the GROMACS Wizard tutorial.

From this tutorial you will learn how to prepare a coarse-grained (CG) system with GROMACS Wizard, i.e. create a periodic box, solvate it, and add ions, to later be able to run minimization, equilibration, and production MD.

In this tutorial, we will be using a CG system generated by the Martinize2 SAMSON Extension for the MARTINI v.3.0.0 force field, see the Martinize2 tutorial.

Tip

Before proceeding with the tutorial, we recommend you to first go through the GROMACS Wizard - Step 1: Prepare tutorial.

Preparation step#

Below are the steps showing how to prepare a CG system in GROMACS Wizard on an example of a soluble protein for which a CG system has been generated in the Martinize2 tutorial.

  1. In GROMACS Wizard, go to the Prepare tab.

  2. In the Set system switch the From to Folder.

    Set system from system folder

  3. Choose a folder with input files: click Browse… and choose the folder with a CG model which contains structure and topology files (.pdb and .top).

    Note

    If you used Martinize2 to generate the CG model, then choose a folder with the generated output results - it should be a folder that contains the generated *_CG.pdb, *_CG.top, etc.

    Choose a folder with a CG model

  4. After you selected the folder, you should see below the PDB, TOP, and ITP files detected in the folder. These files will be used for the system preparation in GROMACS Wizard.

    List of input files

  5. Click the Load button next to the detected PDB file. This is necessary to compute the periodic box for the system. Once clicked, the system will be loaded into a new document and a periodic box will be computed for it as shown in the image below:

    Computed periodic box

  6. If the CG system was prepared by Martinize2, then GROMACS Wizard will automatically switch the force field to martini_v.3.0.0 that it ships, and it will set the solvent model to the default Martini water. Please ensure that the force field was switch to martini_v.3.0.0.

    Choose MARTINI v.3.0.0 force field

    Note

    If you used another CG force field, then you will need to provide it, see Step 1: Prepare - Using a custom force field.

  7. If you want to solvate the CG system, then check the Add solvent options and then click on the options/gear button (Add solvent options) next to it.

    Open solvent options

    In the pop-up window, increase the default van der Waals distance to avoid clashes and ensure proper solvent density – you need to increase it to e.g. 0.21 nm. This is necessary, because GROMACS does not have van der Waals distances defined for CG models and, in this case, it will be using the default van der Waals distance value (0.105 nm) which might be too close for CG beads since each Martini water bead represents 4 water molecules. You can leave other options with default values.

    Solvent options

    Note

    You can also provide a custom CG solvent model, see Step 1: Prepare - Using a custom solvent model.

  8. Change the periodic box size if necessary. For example, you can increase the solute-box distance (note that it should be at least 1 nm to ensure the minimum distance between images) or change the unit cell type to Rhombic dodecahedron, the smallest and the most regular space-filling unit cell.

    See also

    Step 1: Prepare - Defining the box

  9. Neutralize / Add additional ions. Choose positive and negative ions. Ions will be added to neutralize the system. If you want to add additional ions, e.g. via the salt concentration – choose the option and provide parameters.

    Add ions - Salt concentration

    Note

    To neutralize the system or add ions, you need to check the option to add solvent, since ions are added by replacing solvent molecules.

    See also

    Step 1: Prepare - Neutralizing the system

  10. Click Prepare.

    See also

    Step 1: Prepare - Run preparation

  11. You can choose to load the prepared structure and inspect it or proceed directly to minimization. In the document, you can find a folder with the existing index groups created by GROMACS – you can double-click on them to select the associated atomic structures.

Prepared CG system

Note

SAMSON tries to detect CG systems when loading files to visualize them as connected beads. It also colorizes water in blue and ion beads with CPK colors for their corresponding atoms.

Minimization, Equilibration, Production MD#

Once you prepared the system and verified it, switch to the Minimize tab and click on the auto-fill button (Auto-fill button) – this will set the results of the previous run as the input structure for this step.

Minimize: auto-fill from the previous step

Access all the parameters by clicking on All... (Open all preferences) in the Parameters box.

In the advanced parameters window, you can also find the position restraints options in Preprocessing which are automatically filled based on your system (i.e., based on POSRES* defines in topology files). You can apply the position restraints for minimization and equilibration steps, in COM Pulling or Umbrella Sampling.

Note

If in Martinize2 you chose to generate position restraints based on backbone or all, then it generates a separate position restraint records per separate molecule (e.g., per separate protein chain) in places them in the corresponding topology files (.itp) numbering them from 0. So, the position restraint POSRES_MOLECULE_0 corresponds to molecule 0 and so on. If in Martinize2 you chose to not generate position restraints (option none) then there will be no position restraints.

Preprocessing options: POSRES defines

See also

See more info in the tutorials dedicated to these steps: