RMSD graph after protein protein md simulation

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Sat, 06 Sep 2025 07:05:07 +0000
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I did protein-protein MD simulation and did equilibration for 500ns. First for 200ns then extended till 500ns. After pbc mol, centering,in RMSD i see the graph is fluctuating, till 250ns apprx. the rmsd is stable then sudden jumps in 300 ns and stable till 500ns. I checked the trajectory motions and I observed, till 200-250ns the protein stays in complex but after that it drifts apart and stay unbound till 500ns. Is this normal? the production run trajectory motions also showed unbound state over 500ns run. is this normal? or i have to apply gentle force to the system to keep it together? Whats the point of the complex if it drifts apart and stays independent?

I am unable to understand what to do? should i go for fresh run or any other possible solution? I need suggestions on this.

I attached the initial 200ns quilibration run and then extended equilibration run. also the rmsd production rmsd.

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