GROMACS Wizard – Step 5: Production Molecular Dynamics Simulation

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This section is a part of the GROMACS Wizard tutorial.

Once the equilibration of the system is completed – the system’s temperature and density have stabilized at the desired values – we can finally run a production molecular dynamics (MD) simulation.

Switch to the Simulate tab.

Selecting input structure

When launching the Production MD step, GROMACS Wizard requires you to provide a path to a GRO file resulting from the previous step: either a GRO file resulting from the NPT Equilibration step or from the previous launch of the Production MD step. If you want to proceed from the previous step you can simply click on the Auto-fill button highlighted in the image below. This will set the GRO file from the previous successful run (e.g. from the NPT Equilibration step).

You can also choose the input GRO file yourself by clicking on the button.

Choosing parameters

Most of the GROMACS molecular dynamics parameters are presented in the Parameters section of the Simulate tab. By default, these parameters are populated with default values. You can modify these parameters as needed. In the Parameters section, you will find the parameters that are most likely to be changed often, like the algorithm, the time step, the number of steps, and the saving interval.

For the sake of this tutorial, leave the parameters to their default values and set the maximum number of steps to 50 000 because the simulation may take a while. For example, the system in the tutorial has approximately 23 000 atoms and the 50 000 time steps of simulation on a machine with 8 cores would take about 10 minutes.

The other GROMACS molecular dynamics parameters can be accessed by clicking on the All… button. To learn more on how to apply custom parameters please check the Applying custom parameters section.

If you modified some parameters, you can always restore them to their default values by clicking on the Reset button in the Advanced parameters window, or you can load them from an MDP file from some other project using the Load from file… button.

Run Production MD

GROMACS Wizard Extension provides you with the possibility to launch simulation locally on your machine, or in the Cloud, or to generate the input files that you can use to launch computations yourself on your cluster.

In this tutorial, we will be launching computations locally. To learn how to launch computations in the Cloud using GROMACS Wizard please read the Launching computations in the Cloud section of the tutorial.

Now, simply click on the Simulate locally button to launch the Production MD calculations locally on your machine.

Some pop-ups might appear informing you about the current steps or possible issues if there are any.

Please note that during these calculations you can still use SAMSON thanks to the job manager of the GROMACS Wizard Extension.

Please note that depending on your machine and on the number of atoms in your system, this simulation may take a while. For example, the system in the tutorial has approximately 23 000 atoms and the 50 000 time steps of simulation on a machine with 8 cores would take about 10 minutes.

Results

Importing the results

After the computation is done several pop-ups will appear asking for import options and plotting options.

The first pop-up asks about trajectory processing options for plots.

The second pop-up asks about options for creating the RMSD plot.

The third pop-up asks about options for creating the radius of gyration plot.

After that, a pop-up will appear asking for the trajectory import options. You can choose whether to import the whole trajectory, only the last frame, or some range of frames, what type of Periodic Boundary Condition treatment to apply, and on what to center the system. For example, as shown in the image below, you can choose to import only a range of frames and to center the system on the Protein.

If you do not want to import the trajectory you can simply click Cancel – this will not delete any results and will still generate the plots.

You can access the results in the Results folder specified at the top of the GROMACS Wizard. The folders with results are named with the date and time, and the step description (for the Production MD step, the folder suffix is _md).

Plots

After the simulation is finished, two plots will be generated to help you analyze your production simulation. The first one shows the evolution of the radius of gyration. You will be asked for which groups present in the system you would like to create these plots. The second plot is the RMSD of your structure backbone relative to the structure backbone present in the initial equilibrated system.

The plots are automatically generated and saved when the job is finished and the results are loaded. If you would like to save a plot, click on the Save button on top of the figure.

 

Previous: GROMACS Wizard – Step 4: NPT Equilibration
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