GROMACS Wizard – Step 4: NPT Equilibration

FacebooktwitterlinkedinmailFacebooktwitterlinkedinmail

This section is a part of the GROMACS Wizard tutorial.

Once the system’s temperature has stabilized at the desired value, it is necessary to apply pressure to the system until it reaches the correct density. This second equilibration phase is aimed at stabilizing the system’s density at the desired value by performing equilibration using the NPT ensemble (constant Number of particles, Pressure, and Temperature) also known as “isothermal-isobaric”.

Switch to the Equilibrate (NPT) tab.

Selecting input structure

When launching the NPT 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 NVT Equilibration step or from the previous launch of the NPT Equilibration step if the system has not reached the desired density. 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 NVT 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 NPT 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 upon the size and contents of the system, but in NPT, the running average of the density of the system should reach a plateau at the desired value. Typically, 100 ps should be a good start. Please note that pressure is a quantity that fluctuates widely over the course of equilibration or simulation. If the density has not yet stabilized (i.e. the pressure-related terms are slow to converge) in the given timeframe, additional time will be required – you can run the NPT equilibration step again by providing the input data from the previous NPT 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.

Run NPT Equilibration

GROMACS Wizard Extension provides you with the possibility to launch equilibration 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 Equilibrate locally button to launch the NPT 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 10 minutes. For the system in the tutorial, NPT equilibration will take approximately the same time as NVT equilibration.

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 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 NPT Equilibration step, the folder suffix is _npt).

Plots

You can check the plots describing the evolution of the system’s pressure and density over simulation time at the bottom of the tab in the Plots section.

In this example, this plot demonstrates that the density is stabilized at 1030 kg/m3 which is close to the experimental value of 1000 kg/m3 and the expected density of the SPC/E model is about 1008 kg/m3. We can see that the density values are stable over time, indicating that the system is well-equilibrated now with respect to pressure and density.

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

Once the system’s density has stabilized at the desired value, we will proceed to the actual simulation.

 

Previous: GROMACS Wizard – Step 3: NVT Equilibration Next: GROMACS Wizard – Step 5: Production Molecular Dynamics Simulation
FacebooktwitterlinkedinmailFacebooktwitterlinkedinmail

Comments are closed.