# Dumps in protein\_lig of RMSD after MD Simulations **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [February 13, 2024, 8:55am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326 "2024-02-13T08:55:14Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![venukrishna](https://avatars.discourse-cdn.com/v4/letter/v/4af34b/32.png) [@venukrishna](https://gromacs.bioexcel.eu/u/venukrishna)\ **Post date:** [February 13, 2024, 8:55am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/1 "2024-02-13T08:55:14Z")
GROMACS version:2023.3 GROMACS modification: Yes/No Here post your question We are completed MD simulation of protein-ligand complex. After the MD simulation results we observed bumps in RMSD of protein\_lig complex plot but protein is normal. The bumps are good or bad for research or publishing? Can you suggest and am new for MD Simulations. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/841f0cbf9eb9b08c78c66b6299957274f70f6133.png) ---
**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, 7:43pm UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/2 "2024-02-13T19:43:05Z")
Did you account for the periodic boundary conditions (example of how to do it is in this tutorial: [Lysozyme in Water](http://www.mdtutorials.com/gmx/lysozyme/09_analysis.html))? If you have and it’s still resulting in unexpected bumps, try visualizing the trajectory with software like VMD to see if you can identify what’s going on ---
**Author:** ![venukrishna](https://avatars.discourse-cdn.com/v4/letter/v/4af34b/32.png) [@venukrishna](https://gromacs.bioexcel.eu/u/venukrishna)\ **Post date:** [February 15, 2024, 5:10am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/3 "2024-02-15T05:10:44Z")
Thankyou for your response Karis. We are visualizing the Coordination file (solv.gro) and we are identify protein is not completely dissolved in solvation part. It is a reason for bumps in RMSD ? please solve this problem. ![Screenshot 2024-02-15 103137](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/243683f35ff0066800c59ad1f86040c428b813be.jpeg) ---
**Author:** ![venukrishna](https://avatars.discourse-cdn.com/v4/letter/v/4af34b/32.png) [@venukrishna](https://gromacs.bioexcel.eu/u/venukrishna)\ **Post date:** [February 15, 2024, 5:42am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/4 "2024-02-15T05:42:57Z")
After the MD Simulations this is my md.gro file. ![md.gro](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/cf0022f2ba5788f0cbb4ef49278fb57674c589f6.jpeg) ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [February 15, 2024, 5:58am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/5 "2024-02-15T05:58:26Z")
Try visualizing the molecule at the time points where the jumps occur (you can use [gmx trjconv](https://manual.gromacs.org/documentation/current/onlinehelp/gmx-trjconv.html) to extract .gro files at specific time points of a trajectory using -dump) and compare to other points to see what might have gone wrong. In that documentation, you will also find alternative methods to deal with pbc if -pbc mol doesn’t seem to be working (sometimes I’ve found -pbc nojump works when -pbc mol doesn’t) ---
**Author:** ![venukrishna](https://avatars.discourse-cdn.com/v4/letter/v/4af34b/32.png) [@venukrishna](https://gromacs.bioexcel.eu/u/venukrishna)\ **Post date:** [February 15, 2024, 6:06am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/6 "2024-02-15T06:06:12Z")
Thankyou karis. Is it problem protein is out of PBC and its effect MD simulation results? ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [February 15, 2024, 6:27am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/7 "2024-02-15T06:27:44Z")
As long as the box is large enough that the molecule can’t interact with it’s periodic image, pbc won’t affect the actual simulation (going off [Lysozyme in Water](http://www.mdtutorials.com/gmx/lysozyme/03_solvate.html), as long as there’s at least 2 nm between the molecule and it’s periodic image, so based off the pictures you sent, you should be fine) ---
**Author:** ![venukrishna](https://avatars.discourse-cdn.com/v4/letter/v/4af34b/32.png) [@venukrishna](https://gromacs.bioexcel.eu/u/venukrishna)\ **Post date:** [February 15, 2024, 7:14am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/8 "2024-02-15T07:14:23Z")
Thankyou Karis.am using the option gmx\_latest trjconv -s md\_0\_10.tpr -f md\_0\_10.xtc -o md\_0\_10\_new\_center.xtc -center -pbc nojump . again generate the center.xtc file using the nojump option. based on this file after am get RMSD between protein and protein\_lig like this. Is it wrong? ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/7de192701d8ad9c5c376a0ec081d538a6f0d464b.png) ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [February 15, 2024, 7:31am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/9 "2024-02-15T07:31:59Z")
Should be fine ---
**Author:** ![venukrishna](https://avatars.discourse-cdn.com/v4/letter/v/4af34b/32.png) [@venukrishna](https://gromacs.bioexcel.eu/u/venukrishna)\ **Post date:** [February 15, 2024, 7:44am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/10 "2024-02-15T07:44:01Z")
Thankyou Karis. both protein and protein\_lig peaks are similar so can we state that complex is stable as protein? ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [February 15, 2024, 8:20am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/11 "2024-02-15T08:20:29Z")
That RMSD levels off like that does indicate stability, though I’m not familiar enough with your study to provide definitive conclusions beyond what’s already described in this tutorial [Lysozyme in Water](http://www.mdtutorials.com/gmx/lysozyme/09_analysis.html). For further guidance on analyzing protein-ligand interactions, you can refer to this as well [Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/09_analysis.html) ---
**Author:** ![venukrishna](https://avatars.discourse-cdn.com/v4/letter/v/4af34b/32.png) [@venukrishna](https://gromacs.bioexcel.eu/u/venukrishna)\ **Post date:** [February 17, 2024, 11:18am UTC](https://gromacs.bioexcel.eu/t/dumps-in-protein-lig-of-rmsd-after-md-simulations/8326/12 "2024-02-17T11:18:50Z")
Thank you karis