GROMACS version:
GROMACS modification: Yes/No
Hi everyone.
I am new to MD and gromacs. I have just run a 500 ns simulation for an AR and am visualising trajectory data on vmd. My reference structure is equilibration.gro. The protein seems to be rotating within the box (with a rather fixed conformation). In addition, the RMSD plot has huge fluctuations (hits 30 Armstrong).
I was wondering why this problem occurs and how to resolve it.
Many thanks!
you can use gmx trjconv -fit rot+trans to eliminate the rotation. Can you share the rmsd plot?
I think you are computing the RMSD of a full system that includes protein and solvent too. this might be causing the big RMSD. Try to just compute the RMSD of protein backbone and check if it is any different.
I was computing the protein. I tried to compute the protein backbone only and it was still the same.. I can also see the translation and rotation of the protein from the animation film.
Try to clean up the PBCs and center the trajectory with something like this
gmx trjconv -f prod.xtc -s prod.tpr -pbc mol -center -o centered.xtc
and select the protein for centering. Then fit to a decent frame with
gmx trjconv -f centered.xtc -s good.tpr -fit rot+trans -o fitted.xtc
where good.tpr is a tpr of the system where the protein is whole and well positioned (like the one from the energy minimization). For the fit select the Calpha atoms of the backbones of the protein, it should work decently I hope.
It worked! Thank you very much!