# Sudden spike in ligand RMSD during protein-ligand simulation

**URL:** <https://gromacs.bioexcel.eu/t/sudden-spike-in-ligand-rmsd-during-protein-ligand-simulation/9521>\
**Category:** User discussions\
**Created:** [June 27, 2024, 6:01am UTC](https://gromacs.bioexcel.eu/t/sudden-spike-in-ligand-rmsd-during-protein-ligand-simulation/9521 "2024-06-27T06:01:02Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![ShintY](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/shinty/32/3572_2.png) [@ShintY](https://gromacs.bioexcel.eu/u/ShintY)\
**Post date:** [June 27, 2024, 6:01am UTC](https://gromacs.bioexcel.eu/t/sudden-spike-in-ligand-rmsd-during-protein-ligand-simulation/9521/1 "2024-06-27T06:01:02Z")

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GROMACS version:2023.5  
GROMACS modification: No

I recently performed a protein-ligand simulation for 25ns and during the post simulation analysis, I saw a sudden spike in ligand rmsd value which lasted only for about 20-30ps.  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e961b2fd675492742bbe2da49e1dc773fe46c46f.png)

 ![rmsdLIG.600dpi](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/f/f392b21d1c9ac9e9f0bcea318eefbd6057038cb2.jpeg)

Above is the image from ligand-rmsd.xvg file and just below it is a graphical representation of the data. I used gromos54a7ff and used [https://atb.uq.edu.au/index.py](https://atb.uq.edu.au/index.py) to build ligand topology. I’m fairly new into gromacs simulations and from my short experience, never encountered this. I even observed the md-simulation movie on the exact time frame but didn’t observe any abnormal ligand movements.

Any help is appreciated,  
Thank you

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [June 27, 2024, 7:52am UTC](https://gromacs.bioexcel.eu/t/sudden-spike-in-ligand-rmsd-during-protein-ligand-simulation/9521/2 "2024-06-27T07:52:00Z")

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Could you share the pictures of the system for the time frames directly before, at and after the spike?

Also, did you remove the pbc effects and include the -nopbc flag in gmx rms?

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**Author:** ![ShintY](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/shinty/32/3572_2.png) [@ShintY](https://gromacs.bioexcel.eu/u/ShintY)\
**Post date:** [June 27, 2024, 8:39am UTC](https://gromacs.bioexcel.eu/t/sudden-spike-in-ligand-rmsd-during-protein-ligand-simulation/9521/3 "2024-06-27T08:39:05Z")

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Firstly I didn’t remove the PBC while calculating the rmsd. I thought since the protein never touched the pbc boundaried during the entire simulation period, it was unnecessary (please correct me if im wrong).

Below are the pictures of the system, they are in order from 21570-21600ps.

 ![2157](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e5cb9c47c2e5e831bab5f7c82ed4cdd5f28d171d.jpeg)  
 ![2158](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0eea907d37e588d42290aea4e451b203b48123a6.jpeg)  
 ![2159](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/979bd2382046397b5650146d3876fc036e92d978.jpeg)  
 ![2160](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1385d9dd25947eeffab0d20d9ff6b2323ded51f4.jpeg)

The ligand is in RED colour  
Thank you for your response

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<div class="post-metadata">

**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [June 27, 2024, 8:46am UTC](https://gromacs.bioexcel.eu/t/sudden-spike-in-ligand-rmsd-during-protein-ligand-simulation/9521/4 "2024-06-27T08:46:56Z")

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Is there any improvement once you do remove pbc?

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**Author:** ![ShintY](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/shinty/32/3572_2.png) [@ShintY](https://gromacs.bioexcel.eu/u/ShintY)\
**Post date:** [June 27, 2024, 8:54am UTC](https://gromacs.bioexcel.eu/t/sudden-spike-in-ligand-rmsd-during-protein-ligand-simulation/9521/5 "2024-06-27T08:54:11Z")

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Yes there is an improvement  
 ![Screenshot from 2024-06-27 14-21-42](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/7c9409b8110b6d0fd25b12c3aaff770e7d4af09f.png)

But i dont understand why the values spike up that high when neither the ligand nor the protein contact the PBC. Anyways thank you very much sir