This section is a part of the GROMACS Wizard tutorial.
This tutorial demonstrates how to perform COM Pulling using GROMACS Wizard.
Reference: We will use the same system, 2BEG, as in the Umbrella Sampling tutorial by Justin A. Lemkul.
1. Loading the system
First, load the system: go to Home menu > Fetch and load 2BEG from the RCSB PDB in mmCIF or PDB format.
When loading the structure into SAMSON a pop-up might appear with import options depending on the importer. Activate the option “Create a path from multiple models” – when activated, it will load models as a trajectory, else it will load all the models as separate structural models.
Once imported, you should see in the Document view a 2BEG structural model and a 2BEG path (trajectory).
The 2BEG system contains 5 chains, and we will pull chain A away while restraining chain B.
You can see these chains in the Viewport as separate secondary structures. You can reorient the system in the Viewport using the mouse or the Compass in the bottom-left corner of the Viewport. You can activate/deactivate the Compass using the bottom menu in the Viewport. Orient the system as shown in the image below.
The 2BEG system has a trajectory with multiple conformations of the system. To go through conformations, select the path node in the Document view and click Inspect in the context toolbar as shown in the image below.
In the Inspector, you can go through the trajectory’s frames using the controllers. You can use any conformation as the starting one for the tutorial.
2. Pre-processing
Some systems require pre-processing, e.g., removing alternate locations and waters. For the system in the tutorial, you can skip this step since there is no need for such pre-processing. To learn more about this step, please refer to the following tutorial:
3. Preparation
Open the GROMACS Wizard in SAMSON – go to “Home menu > Apps > Biology > GROMACS Wizard” or use “Find everything…“.
Now we need to set up the system for the Prepare step. Below we will briefly cover the steps. To learn more about the preparation step, please refer to the following tutorial:
Specifying the model
- Choose the force field: AMBER03
- Activate the “Add solvent” option and choose the solvent model: TIP3P.
- Activate the “Ignore existing hydrogens” option.
Choosing the system
Next, we need to specify the molecular system:
- Select the 2BEG structural model in the Document View and click “Set system“.
- Leave the “Batch preparation” option non-active.
Defining the box
When setting the box for a pulling simulation, you need to take into account the pulling by leaving enough space in the pulling direction while taking into account the minimum image convention. The pull distance must always be less than half the length of the box along the pulling direction including the periodicity.
Tip: If the pulling direction in your system is not aligned with axes, then you can easily orient the system in SAMSON either using move editors or by right-clicking on the structure and, in the context menu, clicking on “Move selection > Align…” (choose the suitable axis or a plane).
So, in this simulation, we will pull chain A by 5 nm from chain B in the z-direction. Hence, we need to set the length of the box along the z-axis to be at least twice larger than the pulling distance (i.e., at least 10 nm) and we add some additional distance (1nm by each side) to better ensure the minimum image convention if parts of the pulled chain went above 5 nm. Thus, we set the box length in the pulling direction (z-direction) to be 12 nm.
- Choose the “Orthorhombic” unit cell and click “Compute fitted box“. This will compute the box based on the system.
- Choose the “Box lengths” option that allows you to set the box size and set the system size as shown below: 6.5 nm x 4.5 nm x 12 nm.
- Change the center of mass of the system: deactivate the “Center in box” option and set the center to 0.5 x 0.5 x 0.2 of the box size (the values change from 0 to 1).
You can see the visualization of the box directly in the Viewport.
Neutralizing the system
We need to make sure the system is neutral (has zero charge), by adding positive or negative ions. Choose Na and Cl ions and activate the “Neutralize system” option. The simulation will be done in the presence of 100 mM NaCl, on top of neutralizing counterions. For that, activate the “Add additional ions” option, choose “Salt concentration” and set it to 0.1 mol/liter.
Run preparation
You can remove the initial structure by checking the “Remove initial structure” option.
Now it should be all set to prepare the system – click the Prepare button to run the preparation step.
Some pop-ups might appear informing you about the current steps or possible warnings/issues if there are any.
To view the log/output click on the Output button at the top of the GROMACS Wizard:
Results
Once the preparation is finished, an import dialog will appear asking whether you want to import the prepared system into SAMSON. You can import the system to verify if everything is as you expected (box, ions, etc.).
4. Energy Minimization
Switch to the Minimize tab.
To learn more about the minimization step please see:
To proceed from the previous step click the Auto-fill button highlighted in the image below.
Parameters
Open the advanced parameters window by clicking the “All…” button in the Parameters box. In the Preprocessing section, you can see the position restraint options for chains and water – leave them unchecked. For the sake of this tutorial, leave the parameters to their default values. You can reset the parameters to the default ones by clicking on the “Reset” button at the bottom-left of the window.
Run
Click on the Minimize locally button to launch the Energy Minimization 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 energy minimization of the system in the tutorial might take several seconds to about one minute. You can see the current progress in the Output window that should pop up. In the Output window, you can check the output for the potential energy and maximum force – they should be written per step and at the very end of the output.
Once the computation is done, you can skip importing the results.
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.
5. NPT Equilibration
Switch to the Equilibrate (NPT) tab.
To learn more about the NPT equilibration step please see:
To proceed from the previous step click the Auto-fill button highlighted in the image below.
Parameters
Set the parameters as shown in the image below:
Open the advanced parameters window by clicking the “All…” button in the Parameters box. You can reset the parameters to the default ones by clicking on the “Reset” button at the bottom-left of the window.
In the Preprocessing section, you can see the position restraint (POSRES*) options for chains and water – they are filled automatically based on the input system. Activate them for chains as shown in the image below.
Set the Temperature Coupling parameters as shown in the image below (T = 310 K).
In the Velocity Generation section, set the temperature to correspond to the temperature in the Temperature Coupling section.
Leave the Pressure Coupling parameters with their default values.
Run
Click on the Equilibrate locally button to launch the calculations on your PC. For larger systems, you can run the equilibration in the Cloud. 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.
Once the computation is done, you can skip importing the results.
In the Plots section, you can check the plots describing the evolution of the system’s pressure, density, and temperature.
6. Production MD
Switch to the Simulate tab.
To learn more about the Production MD step please see:
GROMACS Wizard – Step 5: Production Molecular Dynamics Simulation
To proceed from the previous step click the Auto-fill button highlighted in the image below.
Add index groups for pulling
If the groups you would like to pull are not present among the default index group generated by GROMACS then you need to add them.
To see the available index groups and to add custom index groups click the “Edit index groups” button.
This will open a window with a list of available default index groups generated by GROMACS. Such groups include, for example, Protein, Water, Ions, etc. You can also add new index groups using this window.
To learn how to add new index groups please refer to:
Important: To add new index groups, it is necessary to load the system in SAMSON – use the “Load” button in the Input section to import the structure. This will facilitate the creation of index groups based on the selections in SAMSON.
For this tutorial, we need to add 2 new index groups: chain A and chain B – since we will be pulling chain A from chain B. Let’s add the first group with chain A:
- Select chain A in the Document view.
- In the Index Groups window (open the window again if it becomes hidden), click “Generate based on current selection in document“. This will generate a selection string for you.
- Set the name to “ChainA”.
- Click “Add index group to the list”.
Let’s now add the second group with chain B.
- Select chain B in the Document view.
- In the Index Groups window (open the window again if it becomes hidden), click “Generate based on current selection in document“. This will generate a selection string for you.
- Set the name to “ChainB”.
- Click “Add index group to the list”.
You should now see two groups in the list of custom groups.
You can check index groups – select one from the list and click “Select in document based on selection string”.
Parameters
Set the parameters as shown in the image below – we will simulate for 0.5 ns with the 2 fs timestep.
Open the advanced parameters window by clicking the “All…” button in the Parameters box. You can reset the parameters to the default ones by clicking on the “Reset” button at the bottom-left of the window.
In the Preprocessing section, you can see the position restraint (POSRES*) options for chains and water – they are filled automatically based on the input system. Activate position restraint for chain B such that it stays in place when chain A is pulled away.
Set temperature and pressure coupling parameters as in the NPT equilibration step.
You can set the output control parameters as in the image below.
Now we need to specify the COM pulling parameters to do the pulling!
Switch to the “COM pulling” section and click the plus button highlighted in the image below to add a new COM pulling group.
We will pull chain A from chain B in the z-direction for 5 nm in 0.5 ns. Populate the COM pulling parameters as follows:
- type: umbrella
- geometry: distance
- group 1: chain A
- group 2: chain B
- start: yes
- distance: N N Y (i.e., pulling in the z-direction)
- init: 0 nm
- rate: 0.01 nm/ps (i.e., 5 nm in 0.5 ns)
- force constant: 1000 kJ mol^-1 nm^-2
Click OK to save the parameters.
Run
You can simulate locally or in the Cloud. Click 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 some time – on a machine with 32 cores it took about 12 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.
If you have only a single project launched then, once it is finished, you will be asked whether you want to import them.
You can load the resulting trajectory in SAMSON to visualize the pulling.
Two additional plots will be generated showing the pull force and coordinates. From these plots, you can see the displacement along the pull coordinate in time – the force builds up until it is sufficient enough to overcome internal restoring forces between chains.
You can use the results for Umbrella Sampling.