# Unevern spikes in RMSD graphs after MD simulations **URL:** \ **Category:** User discussions\ **Tags:** mdrun, analysis-tools, mdrun-performance\ **Created:** [March 9, 2023, 7:42am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944 "2023-03-09T07:42:21Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![gromacs\_amature](https://avatars.discourse-cdn.com/v4/letter/g/bbe5ce/32.png) [@gromacs\_amature](https://gromacs.bioexcel.eu/u/gromacs_amature)\ **Post date:** [March 9, 2023, 7:42am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944/1 "2023-03-09T07:42:21Z")
GROMACS version:GROMACS - gmx rms, VERSION 5.1.4 ![Graph1](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/9536fcf806133ad8c669b5e33e1ffd0ffd6a92e7.png) ![Graph2](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/166730c05c73ef7bf572f35c5201190fda7e3018.png) GROMACS modification: No **Here post your question** 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 ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [March 9, 2023, 8:39am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944/2 "2023-03-09T08:39:55Z")
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)? ---
**Author:** ![gromacs\_amature](https://avatars.discourse-cdn.com/v4/letter/g/bbe5ce/32.png) [@gromacs\_amature](https://gromacs.bioexcel.eu/u/gromacs_amature)\ **Post date:** [March 22, 2023, 2:36am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944/3 "2023-03-22T02:36:58Z")
yes, 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 ---
**Author:** ![gromacs\_amature](https://avatars.discourse-cdn.com/v4/letter/g/bbe5ce/32.png) [@gromacs\_amature](https://gromacs.bioexcel.eu/u/gromacs_amature)\ **Post date:** [March 22, 2023, 2:41am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944/4 "2023-03-22T02:41:55Z")
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 ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [March 27, 2023, 8:41am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944/5 "2023-03-27T08:41:26Z")
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. ---
**Author:** ![fulvio](https://avatars.discourse-cdn.com/v4/letter/f/a88e57/32.png) [@fulvio](https://gromacs.bioexcel.eu/u/fulvio)\ **Post date:** [January 29, 2024, 11:36am UTC](https://gromacs.bioexcel.eu/t/unevern-spikes-in-rmsd-graphs-after-md-simulations/5944/6 "2024-01-29T11:36:30Z")
Try add pbc -nojump