molecular dynamics basics

In this tutorial, we will revisit one of the examples available in pDynamo3, called aSmallProtein.

In the original tutorial, the program sets up a system containing a small peptide, pdb code: 1UAO (10-residue folded peptide designed by segment statistics), inside a cubic box with a side length of 28 Å, using the OPLS force field.

Here, for the sake of simplicity, we will not repeat the entire system preparation. Instead, we will start directly from the solvated system, which was previously generated by the test examples provided with pDynamo.

• Step 1: Loading your system into EasyHybrid: File

For this simple simulation, we will run only 10,000 steps.

The simulation should take just a few minutes.

Once finished, a new object (set of coordinates) is generated in the project treeview.

Once finished, a new object (set of coordinates) is generated in the project treeview.

a) Access the treeview menu by right-clicking on the project header. Select “Import Data…”

b) Choose the format “pkl folder – pDynamo trajectory” and select the folder created by the molecular dynamics simulation.

c) Click Import.

Using the trajectory visualization tool, notice that the water molecules appear to “escape” from the box. Here, an important comment is needed: we are using periodic boundary conditions, so even though they are represented outside the box, the effect is as if, when leaving one face of the box, the molecule “reappears” on the opposite side. In other words, the water molecules are not diffusing into the vacuum, as the representation might suggest.

If our goal is, for example, to analyze how water molecules interact with the peptide, we must perform the procedure known as reimaging (or wrapping), which in practice relocates the water molecules back inside the box.

Go to Analyses > Reimaging (Wrapping).

Select the coordinates corresponding to the newly imported trajectory.

In this case, it is also convenient to center the peptide in the middle of the box. To do this, using the viewing selection mode by molecule, select the peptide and, in the Reimaging Trajectory window, check the option “Center the selection in the box”.

Click the Reimaging button.

Now, using the same selection, let us calculate how the peptide coordinates fluctuate.

Go to Analyses > RMSD Analysis.

Use the option “Plot using EasyPlot”.

We can improve this fluctuation analysis by aligning the trajectory with reference to the protein atoms (other criteria can also be used).

To do this, go to Analyses > Align Trajectory. Select the coordinates of the trajectory of interest and, using the default settings of the window, click Align.

Repeat the RMSD Analysis using the same criteria and compare the results.

Alternatively, the trajectory can be reloaded in its original condition, and the RMSD can be computed while allowing for translational motion of the molecule within the box—an effect that is minimized when the peptide is centered during the reimaging procedure.**