Could you explain the process by which the RMSD result is created, and provide insight into any noticeable jumps or fluctuations in the data? I'm curious about the underlying reasons behind these patterns.
Ali Salehi It appears that your molecule of interest needs to be centered or made whole before RMSD analysis.
Did you center it? If not, you might want to try out some of these:
- gmx trjconv -s md.tpr -f md.xtc -o md_nopbc_cluster.xtc -pbc cluster
- gmx trjconv -f md_nopbc_cluster.xtc -s md.tpr -o md_whole.xtc -pbc whole
- gmx trjconv -f md_whole.xtc -s md.tpr -o md_final.xtc -pbc mol -center -ur compact
Ali Salehi Those fluctuations after 40ns is unusual....... what all parameters u have used for the simulations..... Also try visualising the trajectory in VMD to see the fluctuations in the complex...
Regards
Thank you for providing the answers. I made a modification to the command (gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center) by changing it to (gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc nojump -center). As a result of this modification, the graph displayed a different outcome.
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