How do You Perform a Proper RMSD Analysis of Molecular Dynamics Trajectory (NAMD)?

Question

[naiem.issa]

Hello Biostars Community,

First time poster here.

For my learning purposes, I have conducted an MD simulation on a small protein without ligands/co-factors (minimized, equilibrated 2 ns, production run 10 ns on CUDA Windows) using NAMD's GUI QwikMD (which is super super useful by the way). Settings included IMPLICIT solvation and 0.145 NaCl with 2-fs step interval. I have the PSF and DCD files for the trajectories, and have used the RMSD tool in VMD to create an RMSD plot (attached PNG file here). 

My question is, am I doing the analysis properly? It is clear from the graph that as production time increases, the RMSD is increasing. And when I look at the video, the protein is moving around (e.g. translating around the screen kind of "floating"). I think this sort of "floating" I'm seeing is what is giving the very high backbone RMSD.

I'm new to this whole thing and just need some advice on how to analyze this properly. Any advice is greatly appreciated.

-Naiem

[naiem.issa]

trying image again here

Answer 1

[sumitmittal49]

Hey,

Sorry for the late answer. I hope you managed to resolve the issue. If not, try aligning the trajectory to the initial first before calculating the RMSD. Hope it helps.