Unevern spikes in RMSD graphs after MD simulations

GROMACS version:GROMACS - gmx rms, VERSION 5.1.4

GROMACS modification: No
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I followed the MD run tutorial from Gromacs. I have also applied position restrain for energy minimization. I checked the log files no load dynamic errors. Why this happens?
The other runs have no peaks and attains threshold after gradual increase.
command used for rmsd: gmx_mpi rms -s filename.tpr -f filename.xtc -o rmsd.xvg -n index.ndx

To be clear, this is from the Lysozyme in Water GROMACS tutorial, correct? Have you accounted for the periodic boundary conditions before calculating the RMSD (gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center)?


  1. gmx_mpi make_ndx -f filename.pdb -o index.ndx

  2. gmx_mpi trjconv -s filename.tpr -pbc mol -f filename.xtc -o recenterd_filename.xtc -center -n index.ndx

  3. gmx_mpi trjconv -f recenterd_filename.xtc -o recenterd_filename.pdb -dump 50000 -s filename.pdb -n index.ndx

I did follow the same protocol, single chain pdb’s looked fine and smooth curve. Only the docked structures have spikes in the RMSD calculations.
How to fix this.
any help is much appreciated

Just to be clear, after that second command, you then ran gmx_mpi rms -s filename.tpr -f recenterd_filename.xtc -o rmsd.xvg -n index.ndx with the recenterd_filename.xtc for the -f option, correct?

Also, have you tried visualizing the files to see whether the docked structure is changing in some significant way? It may be easier to diagnose the issue if we know what the simulation output looks like.

Try add pbc -nojump