I have been performing Molecular Dynamic simulation. While calculating RMSD trajectory for protein and protein + Ligand, there is sudden increase in the trajectory tools. What could be possible reason. I have attached two files here.
hello, did you correct the trajectory by using gmx trjconv -pbc before RMSD?
Hi Suraj,
You see jumps in your RMSD curve because your protein is passing through the periodic boundary in those frames. You cannot fix the PBC in those frames when the protein is split into two. Therefore, instead of choosing the entire protein as an index group, you have to choose a single atom as an index group because an atom cannot be split into two across the periodic boundary.
Make a new index file and select a single C-alpha atom, preferably towards the center of your protein. For example:
gmx make_ndx -f input.gro -o center_atom.ndx
> r 30 & a CA
> q
.. and then use this index group to center your protein
gmx trjconv -f XTC -s TPR -o centered.xtc -pbc mol -center -boxcenter tric -n center_atom.ndx
Hope this helps.
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