Hi,
Thank you very much for the reply.
I followed what you suggested these days but sadly it still didn’t work:
gmx rms -s md_0_1.tpr -f trajout.xtc -o rmsd_trajout.xvg -tu ns
I still got spikes in the RMSD results:
As indicated in the figure, the spikes are different from the previous figure I posted several days ago. My supervisor suspected it was generated because the protein wasn’t structurally aligned with the before-simulation protein, so I just tried to structurally align my protein to the reference one. These are the commands I’ve used:
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center (selecting 1 - Protein and 0 - system to re-center)
gmx trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc -o md_0_1_align.xtc -fit rot+trans (selecting 1 - Protein and 1 - Protein for output)
gmx rms -s md_0_1.tpr -f md_0_1_align.xtc -o rmsd_align.xvg -tu ns (selecting 1 - Protein and 1 - Protein for output)
I’ve also checked the similar page (Structural Realignment) and tried the commands over there but there’re still spikes in my RMSD results as shown above. Now I started to suspect whether the plotting tool I used for generating RMSD was not appropriate. For your information, I used grace (Grace Home) to plot my RMSD from the rmsd.xvg file. The postdocs in my group also suspected perhaps the rescheduling of the HPC cluster I was using caused this result, but it’s still the same after I did some replicates.
Any ideas would be greatly appreciated, since I’ve basically tried every possible solution I could get from my group as well as the forum.
Many thanks.