High fluctuation in rmsd of apoprotein

[era01]

GROMACS version: 2023.1
GROMACS modification: Yes/No
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Hi, I am new to this so kindly please help me out on this. i have performed md simulation for both apo protein and complex. for complex I got proper rmsd value but for my apo protein I got very high fluctuations. in the VMD tool I inserted md.gro and md.xtc file and saw my protein was out of the box.and I have observed that this only happened for protein that contained more than one chain.

any idea how I can solve this? i followed the “lysosome in water” tutorial Lysozyme in Water
these are the last two commands I used :
gmx mdrun -v -deffnm md_0_1

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center

(1& 0)

[wilzzw]

It looks like the RMSD jumps might be due to generic artifact of representation of the protein inside the box.

If your protein have more than one chain, consider doing -pbc cluster.
Sometimes trjconv -pbc doesn’t give the desired representation, and I found I have to try a few ways.

[era01]

hello. THANK YOU SO SO SO MUCH. IT FIXED MY PROBLEM. THANKS A LOT FOR HELPING