I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10 windows with 1 Angstrom in each window and 0.1 Angstrom/bin for 18 ns in each window, the PMF profile looks different(pmf_merge.png). Can anyone help me with any analysis to check if the simulations have converged and to check if the plot is correct ?
Thanking you
Gauri
Also can we run different length of simulation in each window. I had initially targeted for force samples collected in each bin to 10^5, but in some of the windows the number of force samples collected were less, so does that mean I should increase the amount of simulation in each window ?
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