GROMACS Wizard – Step 2: Energy Minimization

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This section is a part of the GROMACS Wizard tutorial.

Once the system has been successfully prepared, it is necessary to perform the Energy Minimization (EM) step to ensure that the system has no steric clashes or inappropriate geometry.

Switch to the Minimize tab.

Content

Selecting input structure

When launching the Energy Minimization 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 Preparation step or from the previous launch of the Energy Minimization 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 Preparation 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 Minimize tab. By default, these parameters are populated with default values that are suitable for usual energy minimization runs. 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 energy minimization tolerance.

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

For the sake of this tutorial, leave the parameters to their default values. 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.

Please note that depending on your machine and on the number of atoms in your system, equilibration may take a while. For example, the system in the tutorial has approximately 23 000 atoms and the 50 000 time steps of equilibration on a machine with 8 cores would take about 8 minutes, so for the sake of the tutorial, you can decrease the maximum number of steps to e.g. 25 000.

Run energy minimization

Now, simply click on the Minimize button to launch the Energy Minimization calculations.

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

Depending on your PC, the energy minimization of the system in the tutorial might take about one minute. You can see the current progress in the Output window.

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

Importing the results

After the computation is done a pop-up will appear asking for 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 the last frame 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 plot.

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 Energy Minimization step, the folder suffix is _em).

Plots

You can check the plot describing the evolution of the system’s potential energy, Epot, over the Energy Minimization steps at the bottom of the tab in the Plots section.

In this example, this plot demonstrates the nice, steady convergence of the potential energy.

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

Checking results

There are two important factors to check to determine if Energy Minimization was successful and has converged:
Potential energy – Epot, which should be negative, and (for a simple protein in water) on the order of 105-106, depending on the system size and number of water molecules.
Maximum force – Fmax, the target for which is set in the advanced parameters of the Energy Minimization step (see the description below). For example, “emtol = 1000.0” indicates a target Fmax of no greater than 1000 kJ mol-1 nm-1. Please see tooltips in the advanced parameters.

Please check the output for the potential energy and maximum force – they should be written per each step and at the very end of the output. You can check them in the Output window.

It is possible that Energy Minimization would reach the given maximum number of the Energy Minimization steps and will arrive at a reasonable Epot but with Fmax > emtol. If this happens, your system may not be stable enough for further equilibration and simulation. You might need to evaluate why it may be happening, and increase the number of minimization steps (or run minimization again by providing the input data from the previous minimization step), or change the minimization parameters (integrator, emstep, etc).

 

Previous: GROMACS Wizard – Step 1: Prepare Next: GROMACS Wizard – Step 3: NVT Equilibration
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