Steered MD of protein-protein

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1

GROMACS version: 2018.8
GROMACS modification: No
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I am trying to perform SMD. System have protein with 2 chains i.e. A & B. I am pulling the chain B towards z direction. But chain B doesn’t completely separates from chain A. I have used pull coord1_k from 1000 to 5000 kJ mol-1 nm-2 ; (pull rate 0.01 nm per ps) . Attaching the pullf. xvg graphs and final snapshots after SMD. The terminal part of chain B reamins attached to chain A even after completion of SMD. On analysis i found that Initailly both chain interact with each other via 7 salt bridges, 19 hydrogen bonds. What strategy should i use in this situation? I am pulling the chain to distance of 5 nm towards z direction. Applied restrain on Chain A.
Chain A also have a cofactor GDP. This cofactor doesn’t really interact directly with chain B. But it is somewhat nearer to chain B.

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(Black-1000, Red-2000, Green-3000, Blue-4000)
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Please help!
@alevilla @jalemkul @milosz.wieczor @scinikhil

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Did you tried increasing the distance from 5 nm? @navneetcdl

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Hi! Thank you for reply.

Yes I did, till 9 nm. But it is too long period to get convergence during umbrella sampling. I will end with many configurations. Isn’t it?
Even after doing increasing the length of separation its not getting dissociated. It look like protein is getting streched and unwind. Its like deformed.

What else option I have.

I am still wondering what will be an ideal pull rate, spring constant and separation distance?
@scinikhil can it be a short distance problem, that its not seprated?