Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel.
I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with reasonabvle overlap. Then I used g_wham for plotting PMF considering first 300ps as equilibration. I am getting a plot , but potential is increasing constantly. ie, PMF is not converged as mentioned the tutorial? Do I need to extend the sampling ? or any other reason? Please help me. Thank you. -Aswathy
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