In molecular dynamics (MD) simulations, the "jumping" or distortion of proteins in trajectory videos often occurs due to periodic boundary conditions (PBC), where the protein crosses the simulation box edge and reappears on the opposite side, creating visual discontinuities. Another possible cause is insufficient energy minimization or equilibration, leading to unstable initial configurations. To correct these artifacts, you can re-center the protein in the box using GROMACS commands like echo 1 0 | gmx trjconv -f trajectory.xtc -s topol.tpr -pbc mol -center -o centered.xtc, which removes jumps by accounting for PBC. Additionally, you can rotate the protein to eliminate rotation-induced distortions with echo 1 0 | gmx trjconv -f centered.xtc -s topol.tpr -fit rot+trans -o fitted.xtc, aligning it to a reference structure such as the first frame.

Once the trajectory is corrected, you can proceed with essential post-simulation analyses. For RMSD (Root Mean Square Deviation), which measures structural stability over time, use echo 4 4 | gmx rms -f fitted.xtc -s topol.tpr -o rmsd.xvg, selecting the protein backbone for alignment and comparison. For RMSF (Root Mean Square Fluctuation), which quantifies residue flexibility, run echo 4 | gmx rmsf -f fitted.xtc -s topol.tpr -o rmsf.xvg -res to obtain per-residue fluctuations. Finally, visualize the results using tools like Grace/XmGrace or Python/Matplotlib by plotting the .xvg files to analyze stability and flexibility trends. Proper PBC handling and equilibration ensure reliable post-simulation analysis.

Renuka devi J Proteins "jumping" or appearing distorted in molecular dynamics (MD) simulations is an artifact caused by periodicity and a lack of proper trajectory unwrapping.

What causes these artifacts?

MD simulations typically use periodic boundary conditions (PBC) to mimic an infinite system. This means that when a molecule exits one side of the simulation box, it re-enters on the opposite side. This is seamless from the perspective of the simulation engine. However, if the trajectory video is viewed without correcting for this, the protein might appear to "jump" from one side of the box to the other, creating a visual artifact.

Another cause is when the protein or a large part of it diffuses across the boundary and is displayed on the other side. Over time, parts of the protein might even span multiple periodic images, leading to a visually "torn" or distorted appearance.

How to correct these artifacts?

These artifacts can be corrected by "unwrapping" or "imaging" the trajectory. This process re-centers the protein or a specific group of atoms in the simulation box, making its movement continuous. The corrected trajectory provides a more realistic visualization of the protein's diffusion and conformational changes.

To correct this in GROMACS, you can use the gmx trjconv tool. The key options for this are:

• -f: Input trajectory file (e.g., .xtc).
• -o: Output trajectory file (e.g., unwrapped.xtc).
• -pbc mol: This command ensures that molecules are kept whole. This is the most common and effective option.
• -center: Centers the selected group (e.g., the protein) in the simulation box.
• -ur compact: This makes the coordinates as compact as possible by moving molecules back into the box.

Here's an example command:

Bash

gmx trjconv -s topol.tpr -f trajectory.xtc -o unwrapped.xtc -pbc mol -center

After running this command, you will be prompted to select a group to center and another group to output. You would typically choose the protein for both. The resulting unwrapped.xtc file will have a corrected trajectory.

Post-simulation analyses with GROMACS

Once you have a corrected (unwrapped) trajectory, you can perform essential post-simulation analyses. It's crucial to use the unwrapped trajectory for these analyses to get physically meaningful results.

RMSD (Root Mean Square Deviation)

RMSD measures the average distance between the atoms of a structure and a reference structure. It is used to quantify a protein's structural stability and conformational changes over time. To calculate RMSD with GROMACS, you use the gmx rms tool.

First, you align the trajectory frames to a reference structure (usually the starting structure or a minimized structure) to remove overall translational and rotational movement. Then, you calculate the RMSD for a specific group of atoms (e.g., the backbone).

Corrected command:

Bash

gmx rms -s start.pdb -f unwrapped.xtc -o rmsd.xvg -fit rot+trans

Here, you would select the backbone for the fit and the backbone again for the RMSD calculation. This command will output the RMSD values over time to the rmsd.xvg file.

RMSF (Root Mean Square Fluctuation)

RMSF measures the fluctuation of individual atoms or residues around their average position over the course of the simulation. It provides insights into the flexibility and dynamics of different parts of the protein.

To calculate RMSF with GROMACS, you use the gmx rmsf tool. The input should be the unwrapped trajectory, as a "jumping" protein would show artificially high fluctuations.

Corrected command:

Bash

gmx rmsf -s topol.tpr -f unwrapped.xtc -o rmsf.xvg -res

This command will prompt you to select a group (e.g., C-alpha) for which to calculate the fluctuations. The -res flag calculates the RMSF per residue. The output file rmsf.xvg will contain the RMSF value for each residue.

Renuka devi J try gmx_trj_qk, it is part of gmx_qk Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...