Understanding RMSD and radius of gyration for an Intrinsically Disordered 30-Residue Peptide

User discussions
1

GROMACS version: 2024
GROMACS modification: No

Hello GROMACS community,

I am analyzing the structural dynamics of a 30-residue intrinsically disordered peptide using MD simulations in GROMACS. To process the trajectory, I applied PBC corrections using:

gmx trjconv -s md.tpr -f md.xtc -o md_pbc.xtc -pbc whole
gmx trjconv -s md.tpr -f md_pbc.xtc -o md_nojump.xtc -pbc nojump
gmx trjconv -s md.tpr -f md_nojump.xtc -o md_center.xtc -center

Then, I computed the RMSD of the peptide and the radius of gyration over time.

My questions are:

  1. My RMSD fluctuates between 0.5 and ~1.5 nm, and there are noticeable oscillations. Does this suggest transient structural compactness, or could it be noise due to high flexibility?
  2. The Rg values range from ~1.3 to 2.0 nm, with some fluctuations. Given that IDPs do not adopt stable secondary structures, is this range reasonable? Could the decreasing trend in Rg suggest transient compaction events?
  3. Beyond RMSD and Rg, what additional analyses would you recommend for understanding the conformational behavior of an IDP in MD simulations? (e.g., clustering, end-to-end distance, dssp, etc.)

I appreciate any insights and feedback!

Thanks in advance.

peptide.Rg
peptide.Rg978×615 5.16 KB

peptideRMSD
peptideRMSD973×569 4.91 KB

2

There are more: RMSD, RMSF, RG, SASA, acylindricity, asphericity, etc.
Check this: 1. https://pubs.acs.org/doi/10.1021/acs.jpcb.4c04901
2. https://doi.org/10.1002/cbic.202400088

3

Thank you for the suggestions! I’ll explore these additional analyses. However, I’d still appreciate insights on my original questions about RMSD fluctuations (transient compactness vs. noise) and Rg trends (whether the range and decreasing trend suggest compaction). Looking forward to your thoughts!