# Simulation Breaks the system (separates both the chains of the Antibody) **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdp-parameters, grompp, mdrun, analysis-tools\ **Created:** [January 19, 2023, 12:49am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601 "2023-01-19T00:49:28Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [January 19, 2023, 12:49am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/1 "2023-01-19T00:49:28Z")
GROMACS version: GROMACS modification: No Hi @jalemkul I have run the MD simulation (protein-lignad) by following your protocol ([http://www.mdtutorials.com/gmx/complex/index.htm](https://mdtutorial)). Also at the end of simulation, I recentered and rewrapped the coordinates using `gmx trjconv` command. In MD simulation movie it gives weird outcome. I ran MD simulation for 200 ns. Energy minimization graph is as follow. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/b2945ca82d899efdbc764a34997f8440af5bf1c3.png) since this portal doesn’t allow to upload video, please follow the link to see the video ([protein\_ligand\_movie.mp4 - Google Drive](https://drive.google.com/file/d/1ml2O7kUp4I-VFHHwms5psc9DUZR63-1M/view?usp=sharing)). Also, I am attaching few frames of it. At the begining: ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/07f244306d9540ca8e5fa18c2dbee3f0a19c53c8.jpeg) after some time (around 50 ns): ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/97f65bfc55075b756ae83c165616ff1fca103b88.jpeg) At near 100ns ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/ca73d9a8a36e94d5ad2fa3f6eebd12ac73b7fbf2.jpeg) at the end of simulation ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1b84367e348c98e23e7dbe56f6d258425254879c.jpeg) Throughout the simulation, both of the chains of Antibody keep joining and separating. Why is this happening? Thanks ---
**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:** [January 27, 2023, 5:36pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/2 "2023-01-27T17:36:32Z")
This is a simple PBC effect. Use `gmx trjconv` to center on one chain (not the default “Protein” group, you need to create an index group corresponding to one of the protein chains). ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [January 31, 2023, 6:00am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/3 "2023-01-31T06:00:42Z")
Thank you @jalemkul First, Do I need to modify the index file by adding a group having atoms of Heavy or Light chain only. Then run the production MD commands. ```auto gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr gmx mdrun -deffnm md_0_10 ``` after MD production, `gmx trjconv` and then select one chain to be centered. If not so could you please help me how to do that? Thanks ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [February 1, 2023, 1:06am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/4 "2023-02-01T01:06:54Z")
> [@jalemkul](#): > > This is a simple PBC effect. Use `gmx trjconv` to center on one chain (not the default “Protein” group, you need to create an index group corresponding to one of the protein chains). After MD simulation, I created a group (light\_chain) in index.ndx file and run the following command. `gmx trjconv -s MD.tpr -f MD.xtc -n index.ndx -o MD_center.xtc -center -pbc mol -ur compact` I selected the following options ```auto select a group for centering-> light_chain select a group for output-> system ``` Upon visualization same result. it separates both the chains apart. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/22a3a767c79a07e83d33f10670a70424cd7bb2ec.png) ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [February 9, 2023, 4:04am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/5 "2023-02-09T04:04:26Z")
Hi Users, @jalemkul Still struggling with this problem. Any help will be appreciated. Thanks ---
**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:** [February 9, 2023, 6:38pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/6 "2023-02-09T18:38:15Z")
Please render the box itself in your image. ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [February 10, 2023, 8:25am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/7 "2023-02-10T08:25:39Z")
Did you mean MD movie having solvent, ion and box? In Chimera, I could’t find a way to get box boundaries. So, I tried it by uploading MD.gro and MD\_recenter.xtc without deleting water/SOL molecules. Please find the url. > **[pro\_lig\_sim.mp4](https://drive.google.com/file/d/1YqgYzOuaUGFCKOsp6_obhGICs6Ot4QaV/view?usp=share_link)** > > Google Drive file. ---
**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:** [February 10, 2023, 2:29pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/8 "2023-02-10T14:29:28Z")
Your simulation box is too small to properly accommodate your protein complex, so one chain hits a periodic boundary and jumps. This is not resolvable via `trjconv` and you need to check your simulation carefully for minimum image violations. ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [February 12, 2023, 4:20am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/9 "2023-02-12T04:20:30Z")
Thanks for the suggestion. How to determine the appropriate size/dimension of the box? I have used the box of same dimensions/size for a protein-protein (macromolecule) MD simulation and that worked perfectly. However, in Protein-Ligand MD simulation I’m facing this issue. I am worried if I choose bigger box than required, lots of water molecule and ions might make simulation unnecessary heavy and this might impact the results. ---
**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:** [February 16, 2023, 2:30pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/10 "2023-02-16T14:30:21Z")
You need a suitable spatial buffer around the solutes to avoid minimum image violations anyway, so if the solute is large, so too will your system. You can use something more efficient than a cubic box, like a rhombic dodecahedron, but `editconf -d 1.0` is typical to get an appropriate box size. ---
**Author:** ![Nik](https://avatars.discourse-cdn.com/v4/letter/n/6de8d8/32.png) [@Nik](https://gromacs.bioexcel.eu/u/Nik)\ **Post date:** [December 24, 2023, 1:03am UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-system-separates-both-the-chains-of-the-antibody/5601/11 "2023-12-24T01:03:38Z")
I also have a similar problem. My system consist of two protein chains (protein-protein complex). After doing the md I see on trajectory that chains are divided and move out of box. I used procedure as for „protein in water”. I ask for help: on which stages and what changes I should make in order to exclude such situation: during protein-protein complex preparation, just before md or after md?