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Iam performing umbrella sampling of a ligand getting pulled towards the binding site and again getting dislogded as the pull force increases
The pulling experiment starts from the ligand getting pulled at -1.6 nm from the chosen center of mass and then it binds somewhere at 0.4 nm. But in PMF graph , i see sampling hapenning at -3nm and the sampling ends at 0 nm. Same goes for the histogram. Actually my pulling simulation runs for 543 ps and I have sampled configuration frames till 450ps. The binding happens somewhere near 405 ps. But still I am not able to correlate ANYTHING. Am I missing anything or have something wrong . Can anyone guide me through
