This section is 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 reaches 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 one of the following:
- The path to a GRO file resulting from the previous step: either a GRO file resulting from the Minimization step or the previous launch of an equilibration step.
- The path to a batch project, that has been minimized or resulted from one of the other steps.
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 automatically fill the path based on the previous project, whether a GRO file or a batch project from the previous successful run (e.g. from the Minimization step).
You can also choose the input GRO file yourself by clicking on the “…” button.
Choosing parameters
GROMACS molecular dynamics parameters for NVT equilibration are present in the Parameters section of the NVT Equilibration 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 integration time step and the number of steps.
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 simply run the NVT equilibration step again by providing the input data from the previous NVT equilibration step.
The other GROMACS molecular dynamics parameters can be accessed by clicking on the “All…” button highlighted in the image above. To learn more on how to apply custom parameters please check the Applying custom parameters section.
Note: The position restraint (POSRES*) options are filled automatically based on the input system.
In the “Temperature coupling” section you can modify the corresponding parameters, such as the thermostat, systems to couple, time constant, and the reference temperature. For most of the projects, you can use temperature coupling using velocity rescaling with a stochastic term, v-rescale, and the time constant of about 1 ps, as shown in the image below. Please note that the temperature for the velocity generation (specified in the “Velocity generation” section) should correspond to the coupling temperature.
You can specify the groups to couple other than the “System”, for example, “Protein non-Protein”. For that click on the “+” button next to the groups to couple – a pop-up dialog will appear from which you can select index groups available in your system. Please note that the number of time constants and reference temperatures should correspond to the number of groups as shown, for example, in the image below.
Note: you can add custom index groups directly from the NVT Equilibration tab by first loading the system (click the “Load” button next to the chosen input GRO file) and then clicking the “Edit index groups” button in the Parameters section. See Adding custom index groups for more information.
You can reset back to the default “System” coupling by clicking on the reset button.
For the sake of this tutorial, reset the parameters to their default values.
To restore the parameters to their default values click on the “Reset” button in the Advanced parameters window. To load the parameters from an MDP file from some other project click the “Load from file…” button. To save the parameters in an MDP file click the “Save as…” button.
Note: the modified parameters are saved on closing SAMSON, so the next time you will have the previously saved parameters.
Run NVT Equilibration
GROMACS Wizard gives you several possibilities:
- Generate inputs – generates a ready-to-use project that you can, for example, run on your local cluster.
- Equilibrate locally – launches the computations locally on your PC using the shipped GROMACS or the one you specified in the settings (see Using custom GROMACS version and performance parameters).
- Equilibrate in the cloud – launches the computations in the cloud. This is suitable for big systems that would otherwise require too many resources to do it locally. This will prompt you to select the Cloud machine, etc. Note that launching in the Cloud requires computing credits. See Launching Computations in the Cloud for more information.
Now, simply click on the Equilibrate locally button to launch the calculations on your PC. Some pop-ups might appear informing you about the current steps or possible warnings/issues if there are any.
Depending on your PC, the equilibration of the system in the tutorial might take a few minutes. You can see the current progress in the Output window that should pop up.
During these calculations, you can still use SAMSON and GROMACS Wizard thanks to the job manager of the GROMACS Wizard Extension. You can always access the list of the local GROMACS jobs and their state via the “Local jobs” button.
Importing the results
If you launched a single project and there are no other projects in the local job queue then after the computations are done a pop-up will appear asking for import options. If you launched multiple jobs or a batch job then you can check their state in the Local jobs. 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 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 launch 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 is 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.
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