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.
(Black-1000, Red-2000, Green-3000, Blue-4000)