# Simulation breaks the side chain of some residue gromacs **URL:** \ **Category:** User discussions\ **Tags:** mdrun, analysis-tools\ **Created:** [February 13, 2024, 7:13pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331 "2024-02-13T19:13:47Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\ **Post date:** [February 13, 2024, 7:13pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331/1 "2024-02-13T19:13:47Z")
GROMACS version: GROMACS modification: Yes/No I have performed 3 replicates of 10 ns protein simulation using the same npt.gro files. replicate 1 seems to be fine but in the other 2 replicates when I visualize the .gro and .xtc file produced after simulation in VMD I can see that for a small number of frames side chains of some residues are detached from the backbone. and in some frames, the Beta sheet becomes so thin like a loop. I cannot understand why it is happening and how to resolve this issue. i have used gromos54a8 forcefield ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [February 13, 2024, 7:32pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331/2 "2024-02-13T19:32:03Z")
The visualization don’t necessarily represent the topology since it only uses distance-based heuristics to place bonds when atoms are close enough ([Bond Dissappearing in VMD - #2 by rpsingh](https://gromacs.bioexcel.eu/t/bond-dissappearing-in-vmd/6009/2)), so weird artefacts like this often appear. As long as the topology file is correct, your simulation should be correct (Gromacs can’t add or remove bonds during the simulation) ---
**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\ **Post date:** [February 14, 2024, 5:46am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331/3 "2024-02-14T05:46:08Z")
thank you for the response. I hjave to make a movie of the trajectory but it seems too fuzzy when one seees such drastic changes in the trajectory. is there a ways that I can see the correct visualization. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [February 14, 2024, 8:53am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331/4 "2024-02-14T08:53:17Z")
VMD should provide a method for adjusting the cutoff distance for bonds which you can adjust, as is suggested here ([[gmx-users] Bonds missing in VMD visualization](https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/RsHir0Wc/gmx-users-bonds-missing-in-vmd-visualization)) which should solve issues with bonds disappearing in the visualization ---
**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\ **Post date:** [February 15, 2024, 4:04pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331/5 "2024-02-15T16:04:20Z")
It must be due to periodic boundary condition issues. You can fix this with the GROMACS suggested workflow: [https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow](https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow) If you are using VMD, check the trajectory smoothing window size to be zero (Graphics \> Representations \> Trajectory tab) as well.