This section is part of the GROMACS Wizard tutorial.
Once the system has been preprocessed and validated we can start the preparation step. In order to launch GROMACS simulations, we first need to prepare the system: choose the model (force field, solvent, ions), and define the periodic box. During the preparation step, GROMACS Wizard will generate a model, and add solvent and ions if necessary.
Choosing the results folder
First, let’s choose a folder where we would like the results to be saved. Click on the … button to choose the folder.
The Open button allows you to quickly open this folder in your default file explorer.
Specifying the model
The next step is to specify the model: choose the force field, solvent model, and provide additional topology files if necessary.
Choosing the force field
Now, we need to choose the force field with which we would like to simulate the system.
Please note, that the choice of the force field is very important and might significantly influence the simulation. Please refer to publications on the force fields and select the one that is most applicable to your system.
For this tutorial, we will be using the all-atom OPLS-AA/L force field. Please choose it from the list of available force fields in the Model section.
Note, that the force field list contains standard force fields that are shipped with GROMACS and also custom force fields that your might have provided before.
If you would like to use a custom force field, please refer to the Using a custom force field section below.
Providing additional topology files
The 1AKI system used in this tutorial does not have any arbitrary molecules so you do not need to apply this step.
If your system contains any arbitrary molecules which you would like to include in the simulation and for which GROMACS cannot generate the topology itself, then you will need to provide topology files for them (itp files). You can generate the topology files for arbitrary molecules using various servers, e.g. the ATB Server or CGenFF server. If you have them then you just need to provide them in GROMACS Wizard and it will do the rest for you.
Please note, that if you provide additional topology files then you will need to provide the force field with which they were parametrized. Please see the Using a custom force field section on how to provide a custom force field.
Using a custom force field
If you want to use a custom force field then you can easily provide it by clicking on the Add button for force fields.
To remove an added force field from the list you can press the Remove button. Please note, that it will remove all the added custom force fields, but the standard force fields will not be removed.
Each force field proposes water models which can be used to describe water molecules if you want to simulate your structure in explicit water.
In this tutorial, we will be using the SPC/E water model. Please choose the SPC/E model from the water model list:
Note, that if you choose “none” as the water model, then the possibility to add solvent and ions will be disabled.
To add explicit solvent in the system, check the Add solvent option as shown below:
Using a custom solvent model
If you want to use a solvent model that is not included with the chosen force field then you can easily provide it by clicking on the Add button for the water model. In the pop-up dialog, you can provide a topology file (.itp) for a new solvent model and, if necessary, a coordinate file (.gro).
How to choose the solvent structure type
If the solvent is a 3-, 4-, or 5-site water model then you can choose the corresponding type from the list without the need of providing the corresponding structure file, in this case, the corresponding standard coordinate files shipped with GROMACS will be used.
Else, you will need to provide a custom coordinate file (.gro) that corresponds to this solvent model. The coordinate structure file should contain a box of solvent molecules equilibrated in periodic boundary conditions to ensure a good alignment of molecules on the stacking interfaces. The box of solute is then built by stacking the coordinates read from the coordinate file.
To remove an added solvent model from the list you can press the Remove button. Please note, that it will remove all the added custom solvent models from the chosen force field, but the standard water models provided with the force field will not be removed.
If your system contains hydrogens you might choose to ignore them by checking the associated box in the Model section.
This is especially useful for NMR structures. Otherwise, if hydrogen atoms are present, they must be named exactly how the force field that you chose in GROMACS expects them to be named (please check the chosen force field conventions). If you need to preserve hydrogens in the system as they are, then do not apply this option and make sure that all the hydrogens in the system are set properly.
We recommend ignoring existing hydrogens – GROMACS will then add them using the selected force field naming convention (note that not all the present force fields might have the same H atoms naming convention).
Defining the box
Now we need to define the box before proceeding with the preparation step.
To define the box, select the system from the Document view or leave the selection empty if you would like to prepare the whole system in your document.
There are several types of unit cells that are supported:
- Rhombic dodecahedron,
- Truncated octahedron.
Please refer to GROMACS Wizard: Periodic boundary conditions for more information.
For the sake of the tutorial, choose the Cubic unit cell and then click the Compute fitted box.
This will automatically generate the chosen unit cell (its positions and size) that fits tightly to your system. All the atoms of your selected system will be included in the box because the box dimensions are determined based on the size of your system (in x, y, z).
Once you have generated your box, you can easily change its size by modifying the corresponding unit cell parameters.
We need to increase the box size to add enough additional space between the system (without solvent) and the box edges. Since the periodic boundary conditions are used it is crucial to satisfy the minimum image convention. This means that, for example, a protein should never see its periodic image, otherwise the calculated forces might be wrong. We recommend adding an additional distance of at least 1.0 nm – that would mean that there is at least 2.0 nm between any two periodic images of a protein or other non-solvent molecules (please note that molecules in the system, e.g. a protein, might go through various conformations). This distance should be sufficient for just about any cutoff scheme commonly used in simulations but you might need to verify with the force field paper if you are using a custom force field.
Now, increase the box size by 2 nm. You can do it by increasing the box length:
or by specifying the required solute-box distance – you will see the new size of the box next to it:
Note, that when loading GROMACS results, SAMSON will try to automatically detect the type of the unit cell of the system, but you can always modify it in the importer dialog which appears on loading of GROMACS trajectories.
Neutralizing the system
We need to make sure the system is neutral, by adding positive or negative ions.
Note: ions are added to the system as a replacement for water molecules, so solvation is required.
To neutralize the system, check the Neutralize system option as shown below:
The neutralization will be done automatically by GROMACS.
Each force field proposes a set of positive and negative ions for the neutralization of your system by GROMACS. You can choose them from the associated lists. Note that only one type of ions (positive or negative) or none of them will be added by GROMACS based on the total charge of your system.
If you would like to know the total charge of your system before running the preparation step, you can compute it by selecting the system and pressing the Update button. For example, if your system’s total charge is 8, GROMACS will add 8 negative ions to neutralize the system.
Adding additional ions
You have the possibility to increase the ion concentration in your system by adding more ions. To do so, check the Add additional ions option and specify the number of additional positive/negative ions that you would like to be added to the system.
For example, if your system’s total charge is 8, you can ask GROMACS to add 12 additional positive ions thus bearing the total charge of the system to 20. Since GROMACS needs to neutralize the system it will add 20 negative ions during the preparation stage. Therefore, the ions which would be added to your system to neutralize its total charge go from 8 negative ions to 20 negative ions and 12 positive ions.
Please note that ions will be added to your system as a replacement for water molecules.
It is possible to include several structural models in your system. To do so, you can either select the ones you want to include in your system or leave the selection empty to include all of them. If the selection is left empty while several structural models are present in the document, GROMACS Wizard will ask you to choose if you want or not to include all the structural models when preparing the system.
Note, that the box needs to include all the structures selected for the preparation. Please see the Define box section.
Now we should be all set to prepare the system – click the Prepare button to run the preparation step.
Some pop-ups might appear informing you about the current steps or possible issues if there are any.
To view the log/output click on the Output button at the top of the GROMACS Wizard:
Once the preparation is finished, the prepared system will be loaded in SAMSON – a new structural model presenting the prepared GROMACS should be visible in the Document view and in the Viewport.
Note that you can choose to remove the initial structure by checking the Remove initial structure checkbox before clicking the Prepare button.
Let’s now visualize the system. You can visualize yourself step-by-step or you can simply apply one of the available Visual presets. Select the system in the Document view and go to Biology menu > Visualize > Visual preset. Choose the first one as shown in the image below and click OK.
Note, that you can modify existing visual presets and create and save your own presets.
As the result, you should have something like in the image below. You can modify the parameters of the visual models, by selecting them in the Document view – expand the visual preset folder and select a visual model that you want to modify. For example, you can select the Water – Licorice visual model and in the Inspector (Interface menu > Inspector) modify the radius to e.g. 0.07 A.
Please check out the User Guide: Visualizing to learn more on how to add visual models, change rendering, and create publication-quality images.
If you would like to repeat it yourself step-by-step, you can perform the following steps:
1. Select the protein (go to Biology menu > Select > Receptors) and add the secondary structure visual model (Biology menu > Visualize > Ribbons).
3. Select water (go to Biology menu > Select > Water) and add the Licorice visual model (Biology menu > Visualize > Licorice).
2. Select ions (go to Biology menu > Select > Ions > Monatomic ions) and add the Van der Waals visual model (Biology menu > Visualize > Van der Waals (in the same list as Licorice)).
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