# Protein protein complex simulation **URL:** \ **Category:** User discussions\ **Created:** [May 30, 2022, 7:52pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231 "2022-05-30T19:52:01Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![pssahoo](https://avatars.discourse-cdn.com/v4/letter/p/76d3ee/32.png) [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Post date:** [May 30, 2022, 7:52pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/1 "2022-05-30T19:52:01Z")
GROMACS version:No GROMACS modification: No hey, i was trying the md simulation of a protein-protein complex. i followed the lysosome in water tutorial of Lemkul with the given mdp files. after the mdrun im observing an unusual behavior in the RMSD plot. suddenly from 0.5… its increasing to 5.84… So i request for a genuine help. The confusions i stated below… 1. is the protein-protein complex simulation process is same as the Lysosome in water process? 2. is the mdp files used for Lysosome in water simulation will be used in protein-protein mdrun? 3. is OPLS and SPC/E are the appropriate forcefield and water model for protein-protein md run? 4. is there any other procedure for protein-protein complex simulation in gromacs? Looking forward to hearing Regards ---
**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:** [May 31, 2022, 2:49am UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/2 "2022-05-31T02:49:10Z")
Your complex is probably splitting across a periodic boundary. When re-imaging via `gmx trjconv`, center on one subunit rather than just choosing “Protein” for the selection. ---
**Author:** ![pssahoo](https://avatars.discourse-cdn.com/v4/letter/p/76d3ee/32.png) [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Post date:** [May 31, 2022, 4:15am UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/4 "2022-05-31T04:15:36Z")
Hello sir, Thank you for your valuable reply. Im using the gmx trjconv command for recentering : gmx trjconv -s md\_0\_10.tpr -f md\_0\_10.xtc -o md\_0\_10\_center.xtc -center -pbc mol -ur compact. Now its giving me some options for centering. Previously i was choosing protein for centering and system for output but now with your suggestion i selected system for centering. still im facing the same problem. Im confuse that which option should i select for centering. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/45f8161584de9dc11168d3c914275cff125d7e53.png) Looking forward for your kind suggestion. Regards ---
**Author:** ![pssahoo](https://avatars.discourse-cdn.com/v4/letter/p/76d3ee/32.png) [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Post date:** [May 31, 2022, 4:20am UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/5 "2022-05-31T04:20:21Z")
Hello sir, Thank you for your valuable reply. Im using the gmx trjconv command for recentering : gmx trjconv -s md\_0\_10.tpr -f md\_0\_10.xtc -o md\_0\_10\_center.xtc -center -pbc mol -ur compact. Now its giving me some options for centering. Previously i was choosing protein for centering and system for output but now with your suggestion i selected system for centering. still im facing the same problem. Im confuse that which option should i select for centering. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/45f8161584de9dc11168d3c914275cff125d7e53.png) Looking forward for your kind suggestion. Regards ---
**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:** [May 31, 2022, 12:21pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/6 "2022-05-31T12:21:38Z")
You need to create an index group that corresponds to one of the monomers. Please search in this forum for how to work with these systems; this same problem gets asked and answered weekly. ---
**Author:** ![pssahoo](https://avatars.discourse-cdn.com/v4/letter/p/76d3ee/32.png) [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Post date:** [May 31, 2022, 5:17pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/7 "2022-05-31T17:17:33Z")
hello sir, your suggestions are really valuable. I was doing a protein protein complex simulation. Protein\_chain\_A having residue from 31-818 Protein\_chain\_B having residue from 1-183 With your suggestion i indexed only a single monomer i.e protein\_chain\_A with the command gmx make\_ndx -f md.gro -o index.ndx > r 31-818 > q Now it created the index group only for the protein\_chain\_A group. While centering i chooses the newly created index group for centering and system for output. But still im getting the same problem in the RMSD plot. For your consideration i am hence attaching the RMSD plot. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8bc261845346d40c4d3974b34d9fcb9213fd8e72.png) waiting for your kind suggestons Thanking you Regards ---
**Author:** ![pssahoo](https://avatars.discourse-cdn.com/v4/letter/p/76d3ee/32.png) [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Post date:** [May 31, 2022, 6:19pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/8 "2022-05-31T18:19:55Z")
hello sir, With reference to the above mentioned problem i would like to show you the images of md.gro file and the dumped pdb. 1. md.gro ![md.gro](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/383ff16932aefffd8031bf046ad1593ef512b9ba.jpeg) i can correlate the high deviation of RMSD plot with these images. kindly suggest me some valuable rectifications. Looking forward from you Regards ---
**Author:** ![pssahoo](https://avatars.discourse-cdn.com/v4/letter/p/76d3ee/32.png) [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Post date:** [May 31, 2022, 6:21pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/9 "2022-05-31T18:21:14Z")
As a new user i was not allowed to post two pictures in a single reply so posting the second picture here 1. Dumped pdb of the last frame after recentering using gmx trjconv ![dump_pdb](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/06ab8cd30624b07bd6ad0df4f292187ef96f5733.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:** [May 31, 2022, 6:31pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/10 "2022-05-31T18:31:20Z")
> [@pssahoo](#): > > Protein\_chain\_A having residue from 31-818 > Protein\_chain\_B having residue from 1-183 You have overlapping residue numbers in each chain, so you cannot create the index group by selecting via residue number. Select based on the atom numbers, or provide a PDB file that has chain identifiers and select based on chain. ---
**Author:** ![pssahoo](https://avatars.discourse-cdn.com/v4/letter/p/76d3ee/32.png) [@pssahoo](https://gromacs.bioexcel.eu/u/pssahoo)\ **Post date:** [June 1, 2022, 10:59am UTC](https://gromacs.bioexcel.eu/t/protein-protein-complex-simulation/4231/11 "2022-06-01T10:59:00Z")
Hello sir, Thank you so much for your guidance. Indexing a single monomer with the atom numbers also didnt worked for me as there were overlapping in atomic numbers too. However i was successful indexing based on the chain number. Now i can get a stable plot in RMSD chart. This really helped me to overcome my problem. Thanking you Regards