GROMACS version: 2024
GROMACS modification: Yes/No
Here post your question :
Dear all,
This time, I had run a pure protein MD simulation and wanted to try PCA analysis. However, the results turned out to be 0.
I used the GROMACS 2024-version (also tried the 2021-version). The unrestrained MD simulation only ran for 300 ps (in the order of energy minimization, restrained MD, and then regular unrestrained MD).
For the produced ‘md.xtc’ file, I used ‘trjconv’ with the “-pbc mol -center” to process the trajectory, and I selected the ‘protein’ group both two times.
Then, I used ‘trjconv’ again with “-fit rot+trans” to process the trajectory from the previous step, and I selected the ‘protein’ group both two times, resulting in the ‘aligned.xtc’ file.
Finally, I ran the command gmx covar -s md.tpr -f aligned.xtc -o eigenvalues.xvg -v eigenvectors.trr -xpma covar.xpm, and I selected the ‘alpha-C atoms’ both two times.
When I checked the eigenvalues file (eigenvalues.xvg), all the values were 0 (every frame).
Two weeks ago, I also tried a similar simulation with a protein-ligand complex (PDBID:3ATL), and the results were the same—all zeros.
Did I misunderstand something? I really appreciate your help and look forward to your replies.
I think you misunderstood PCA and the eigenvalues. The eigenvalues are not per frame but for each eigenvector. My guess is that you first only analyzed a single frame, which results in a covariance matrix with all zeros and thus the eigenvalues are all zero.