# RMSD shoots up **URL:** \ **Category:** User discussions\ **Created:** [July 22, 2020, 1:34pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556 "2020-07-22T13:34:12Z")\ **Posts on this page:** 19\ **Page:** 1
**Author:** ![veerubiotech](https://avatars.discourse-cdn.com/v4/letter/v/e480ec/32.png) [@veerubiotech](https://gromacs.bioexcel.eu/u/veerubiotech)\ **Post date:** [July 22, 2020, 1:34pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/1 "2020-07-22T13:34:12Z")
GROMACS version: 2020.2 GROMACS modification: Yes/No Here post your question Dear all, I am running a simulation of a complex molecule. it has two chain. When I calculated the rmsd and found that rmsd value shoots up at 16ns and 25ns. In corresponding PDBs two chains are far apart, out of the box. Is it artifacts? if the complex broke at 16ns why it re associates ? How can I fix it? Thank you ![rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/fe71bfc46f6fd8ff7b7a36fd989bb4e3c2016ee1.png) ![step16](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/01d0915d49ae8365edacacc752f8aa0b18ee3ec7.jpeg) ![step25](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/bb620475a5f1e50ed8dfa75f7fd20b70f62d88fe.jpeg) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [July 22, 2020, 1:45pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/2 "2020-07-22T13:45:28Z")
This is a periodicity artifact. Recenter with `trjconv`. ---
**Author:** ![veerubiotech](https://avatars.discourse-cdn.com/v4/letter/v/e480ec/32.png) [@veerubiotech](https://gromacs.bioexcel.eu/u/veerubiotech)\ **Post date:** [August 3, 2020, 10:49am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/3 "2020-08-03T10:49:07Z")
Dear Dr Jalemkul, Following your advice, I combined the xtc file using “gmx trjcat -f step5\_\*.xtc -o combined.xtc -settime” then i tried to remove PBC using " gmx trjconv -s step4.0\_minimization.tpr -f combined.xtc -o md\_0\_1\_noPBC.xtc -pbc mol -center" Then i calculated the rmsd using “gmx rms -s step4.0\_minimization.tpr -f md\_0\_1\_noPBC.xtc -o rmsd1.xvg -tu ns” but still its not centered. the two chains are far apart and rmsd is absurd for these frames. Am I doing anything wrong? Thank you Veeru ![rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/2a67562b67046cb6fa27c1ad6d401a409a1afc7d.jpeg) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 3, 2020, 12:24pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/4 "2020-08-03T12:24:34Z")
[http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow](http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow) For multiple chains, center on one of them, but you will have to do other steps first as suggested in this link. ---
**Author:** ![veerubiotech](https://avatars.discourse-cdn.com/v4/letter/v/e480ec/32.png) [@veerubiotech](https://gromacs.bioexcel.eu/u/veerubiotech)\ **Post date:** [August 3, 2020, 2:10pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/5 "2020-08-03T14:10:51Z")
Thank you Dr Jalemkul. As I am new to Gromacs. I really couldn’t follow the steps given in the link. Is it possible to get set of commnads. Sorry for the trouble. Best regards Veeru ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 3, 2020, 4:43pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/6 "2020-08-03T16:43:04Z")
You will learn lots by reading the `trjconv` help information, which describes everything mentioned in that link :) ---
**Author:** ![veerubiotech](https://avatars.discourse-cdn.com/v4/letter/v/e480ec/32.png) [@veerubiotech](https://gromacs.bioexcel.eu/u/veerubiotech)\ **Post date:** [August 5, 2020, 11:00am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/7 "2020-08-05T11:00:29Z")
Dear Dr Jalemkul, I mange to fix pbc issue. Thanks for your help. I got another question. what is criterion to decide the simulation has saturated? Is the simulation below saturated already at 40ns? as the rmsd plot is flat though i still see small bumps ![rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/9aa4650b4309a17fd95ee47d35d6134f07d3a015.jpeg) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 5, 2020, 3:59pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/8 "2020-08-05T15:59:57Z")
Are you talking about convergence? RMSD doesn’t tell you that. It’s a degenerate metric. You need to examine all relevant structural properties of interest and they should be statistically invariant over time. ---
**Author:** ![Amir.ap](https://avatars.discourse-cdn.com/v4/letter/a/97f17d/32.png) [@Amir.ap](https://gromacs.bioexcel.eu/u/Amir.ap)\ **Post date:** [December 19, 2024, 12:57am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/9 "2024-12-19T00:57:41Z")
Hello there, i have the same problem ( i have RMSD shoot-ups and my protein complex comes out of the box) how can i fix it? shall i do all the steps from beginning? ![Screenshot 2024-12-19 043710](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e97e801cd36ea0e9ac18ef77e16bd3193aa07a72.png) i have check the trajectory file with PYMOL it’s fine until 80 ns how can i fix it? i would be really glad if you help me thanks. ---
**Author:** ![Amir.ap](https://avatars.discourse-cdn.com/v4/letter/a/97f17d/32.png) [@Amir.ap](https://gromacs.bioexcel.eu/u/Amir.ap)\ **Post date:** [January 6, 2025, 10:01pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/10 "2025-01-06T22:01:26Z")
hello, may i ask you how could you over com your issue with your RMSD shoot-ups? was it from complex coming out of the box? thanks. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 7, 2025, 8:48am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/11 "2025-01-07T08:48:36Z")
From the plot it definitely looks like a problem with PBCs. You have to ‘clean-up’ the trajectory with some pre-processing tools like [gmx trjconv](https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html). ---
**Author:** ![Amir.ap](https://avatars.discourse-cdn.com/v4/letter/a/97f17d/32.png) [@Amir.ap](https://gromacs.bioexcel.eu/u/Amir.ap)\ **Post date:** [January 7, 2025, 10:38am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/12 "2025-01-07T10:38:07Z")
thanks for your reply, by ‘clean-up’ you mean what, I’m not sure if i get your point. I have realized that it’s about PBC but I’m not sure how to overcome it. I’ve tried PBC -no jump and other PBC conditions but i think I’m doing something wrong cause I don’t get reasonable result from my system. thanks for your guidance. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 8, 2025, 9:47am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/13 "2025-01-08T09:47:24Z")
With clean-up I mean pre-process the trajectory for data analysis. Sometimes it is not needed and sometimes, like in your case, is mandatory, depending on the analysis you want to carry out. You have to remove the effect of PBCs. You have to play around with `trjconv` and various flags like `-pbc mol`, `-pbc nojump`, and some centering, probably. What do you mean with “reasonable results”? The spikes you have in the plot you posted are clearly artifacts. Then, whether the RMSD values are reasonable or not (spikes excluded), that I do not know. ---
**Author:** ![Amir.ap](https://avatars.discourse-cdn.com/v4/letter/a/97f17d/32.png) [@Amir.ap](https://gromacs.bioexcel.eu/u/Amir.ap)\ **Post date:** [January 11, 2025, 11:58am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/14 "2025-01-11T11:58:53Z")
Hello again and thanks for your reply, I’ve tried few options around trjconv as you said in some cases RMSD goes around 22 A and in some cases it plays around 1 A but the box shatters I’m not sure if it’s alright or not? i want to get these data: RMSD, RDF, RMSF, binding energy and if possible SASA. I would be really glad if you help me out. P.S: when i tried -nojump sol of box get disrupted. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 11, 2025, 12:02pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/15 "2025-01-11T12:02:28Z")
What do you mean with the box shatters? ---
**Author:** ![Amir.ap](https://avatars.discourse-cdn.com/v4/letter/a/97f17d/32.png) [@Amir.ap](https://gromacs.bioexcel.eu/u/Amir.ap)\ **Post date:** [January 11, 2025, 12:03pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/16 "2025-01-11T12:03:48Z")
solvent doesn’t look like a proper box. ---
**Author:** ![Amir.ap](https://avatars.discourse-cdn.com/v4/letter/a/97f17d/32.png) [@Amir.ap](https://gromacs.bioexcel.eu/u/Amir.ap)\ **Post date:** [January 11, 2025, 12:11pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/17 "2025-01-11T12:11:05Z")
![Screenshot 2025-01-11 155251](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/d/d68f69a738da4918c5d3264881839745a6496950.jpeg) something like that. the RMSD in this case looks proper though. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 11, 2025, 3:37pm UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/18 "2025-01-11T15:37:25Z")
This is because you used the flag `-pbc nojump`, which unwraps the PBCs and avoids jumps between sides of the box (the reason why you had that artifact in the RMSD plot). This is also reported in the `trjconv` manual > [@gmx trjconv -pbc nojump](#): > > checks if atoms jump across the box and then puts them back. This has the effect that all molecules will remain whole (provided they were whole in the initial conformation). **Note** that this ensures a continuous trajectory but molecules may diffuse out of the box. ---
**Author:** ![tanisha](https://avatars.discourse-cdn.com/v4/letter/t/258eb7/32.png) [@tanisha](https://gromacs.bioexcel.eu/u/tanisha)\ **Post date:** [May 5, 2026, 5:27am UTC](https://gromacs.bioexcel.eu/t/rmsd-shoots-up/556/19 "2026-05-05T05:27:01Z")
Hi, I am facing the exact same problem you were facing earlier with your rmsd graph. Can you please share the commands you have used to fix it? I would be very grateful. Thanks!