# Protein move out of box and RMSD grpah **URL:** \ **Category:** User discussions\ **Created:** [March 20, 2024, 12:06pm UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656 "2024-03-20T12:06:17Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![NMDr](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@NMDr](https://gromacs.bioexcel.eu/u/NMDr)\ **Post date:** [March 20, 2024, 12:06pm UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656/1 "2024-03-20T12:06:17Z")
GROMACS version: GROMACS modification: Yes/No Here post your question ![RMSD](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/6f2d5a5d7b93c88c5226520ec022c57d564958a7.jpeg) i done MD simulation for Free protein and Complex separately. both the structures are coming out of the box. even i tried gmx trjconv -pbc nojumb and -center , -fit rot+trans my RMSD graph like this. can you suggest me what is the mistake how to solve this issue. thanks in advance ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [March 20, 2024, 11:17pm UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656/2 "2024-03-20T23:17:38Z")
make the protein as whole then fix the jump, you need to use [gmx trjconv](https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html) a couple of times to remove all the artifcats please search over pbc issue, there are lots of discsion that help you to use the trjconv tool. you may start with `-pbc mol -center -ur compact` ---
**Author:** ![NMDr](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@NMDr](https://gromacs.bioexcel.eu/u/NMDr)\ **Post date:** [March 26, 2024, 9:45am UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656/3 "2024-03-26T09:45:55Z")
Thank you. even i tried unable to solve. my protein contains two chain while doing md simulation the chain get separated and coming out of the box . ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [March 26, 2024, 11:23pm UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656/4 "2024-03-26T23:23:01Z")
make an index for both chain together and center the chains first. There are no directy way, you need to play around it to get the corrected one, refer the link above. ---
**Author:** ![NMDr](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@NMDr](https://gromacs.bioexcel.eu/u/NMDr)\ **Post date:** [April 4, 2024, 7:01am UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656/5 "2024-04-04T07:01:55Z")
thank you, ```i gmx make_ndx -f complex.gro -o index.ndx 0 System : 3780 atoms 1 Protein : 3727 atoms 2 Protein-H : 1398 atoms 3 C-alpha : 252 atoms 4 Backbone : 756 atoms 5 MainChain : 1006 atoms 6 MainChain+Cb : 1227 atoms 7 MainChain+H : 1247 atoms 8 SideChain : 2480 atoms 9 SideChain-H : 932 atoms 10 Prot-Masses : 3727 atoms 11 non-Protein : 53 atoms 12 Other : 53 atoms 13 UNK : 53 atoms ``` which group should I select to make a chain index ? can you please give a suggestion? ---
**Author:** ![Seyilaxa](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/seyilaxa/32/3136_2.png) [@Seyilaxa](https://gromacs.bioexcel.eu/u/Seyilaxa)\ **Post date:** [April 4, 2024, 7:59am UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656/6 "2024-04-04T07:59:53Z")
One possibly way is to find a residue(or a atom) as close to the center of the complex and locate it in the .gro file.Using make\_ndx to take it into a separate group, then center the group when using trjconv. ---
**Author:** ![NMDr](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@NMDr](https://gromacs.bioexcel.eu/u/NMDr)\ **Post date:** [April 4, 2024, 9:44am UTC](https://gromacs.bioexcel.eu/t/protein-move-out-of-box-and-rmsd-grpah/8656/7 "2024-04-04T09:44:49Z")
Thank you for ur valuable suggetion