GROMACS Wizard – Step 3: NVT Equilibration

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This section is a part of the GROMACS Wizard tutorial.

Once the system has been successfully minimized, it is necessary to Equilibrate the system to bring it to the desired temperature and pressure/density and stabilize it.

Equilibration is often conducted in two phases. The first one is aimed at bringing the system to the desired temperature (the one that you would like to simulate) and stabilizing it by performing equilibration using the NVT ensemble (constant Number of particles, Volume, and Temperature) also referred to as “isothermal-isochoric” or “canonical” ensemble.

After the system reached the desired temperature we will apply the NPT Equilibration step for the system to reach the desired density.

Switch to the Equilibrate (NVT) tab.

Selecting input structure

When launching the NVT Equilibration 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 Energy Minimization step or from the previous launch of the NVT Equilibration step if the system has not reached the desired temperature. 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 Energy Minimization 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 NVT Equilibration 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 maximum number of steps.

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.

The timeframe for such a procedure depends on the size and contents of the system, but in NVT, the running average of the temperature of the system should reach a plateau at the desired value. Typically, 50-100 ps should be sufficient. If the desired temperature has not been achieved or has not yet stabilized, additional time will be required – you can run the NVT equilibration step again by providing the input data from the previous NVT equilibration step.

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 NVT Equilibration

GROMACS Wizard provides you with the possibility to launch equilibration locally on your machine, in the Cloud, or to generate the input files that you can use to launch computations yourself locally outside of SAMSON or 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 Equilibrate locally button to launch the NVT Equilibration 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, 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.

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 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 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 NVT Equilibration step, the folder suffix is _nvt).

Plots

You can check the plot describing the evolution of the system’s temperature over simulation time at the bottom of the tab in the Plots section.

In this example, this plot demonstrates that the temperature is stabilized around 300 K as set by default in the advanced parameters.

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

It is important to check whether the system has reached the desired temperature (based on kinetic energy) and that the temperature stabilized at it. Please note, that the temperature might fluctuate around the desired value. If the system has not reached the desired temperature or has not yet stabilized at it then you would need to launch additional NVT Equilibration starting from the results of this NVT Equilibration. For that, set the input GRO file to the current NVT Equilibration results (you can simply click on the Auto-fill button to set it to the latest results).

Once the system’s temperature has stabilized at the desired value, we will apply the NPT Equilibration step for the system to reach the desired density.

 

Previous: GROMACS Wizard – Step 2: Energy Minimization Next: GROMACS Wizard – Step 4: NPT Equilibration
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