This section is 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 NPT 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 NPT Equilibration step, or the previous production MD launch.
- The path to a batch project, that has been equilibrated or resulted from one of the previous production MD run.
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 NPT Equilibration).
You can also choose the input GRO file yourself by clicking on the “…” button.
Choosing parameters
GROMACS molecular dynamics parameters for NPT equilibration are present in the Parameters section of the NPT 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 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.
Note: Please ensure that the temperature coupling parameters correspond to the ones from the NVT equilibration, and the temperature in the velocity generation (if it is on) as well.
Note: Please ensure that the pressure coupling parameters correspond to the ones from the NPT equilibration.
For the sake of this tutorial, reset the parameters to their default values and set the maximum number of steps to 50,000 as shown in the image above so that the simulation would not take long. For example, the simulation of the system in the tutorial that has approximately 19,000 atoms for 50,000 timesteps takes about a couple of minutes on a machine with 18 cores.
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 Production MD
GROMACS Wizard gives you several possibilities:
- Generate inputs – generates a ready-to-use project that you can, for example, run on your local cluster.
- Simulate 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).
- Simulate in the cloud – launches the computations in the cloud. This is suitable for simulating 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 Simulate 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 simulation 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.
Results
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.
When importing the production MD results, several pop-up dialogs will appear asking for import options and plotting options. The first pop-up asks about options for creating the RMSD plot.
The second pop-up asks about options for creating the gyration radius plot.
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 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 and the second plot is the RMSD of the chosen structures, e.g. the structure’s backbone relative to the structure’s backbone present in the initial equilibrated system.
If you performed a pulling simulation, e.g. for Umbrella Sampling, then two more plots will be generated showing the pull force and coordinates.
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.
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