Hi, I just want to know about the consistency we could obtain in plotting PMF.
I am using Gromacs 4.0.4 MPI version. Trying to find the PMF of the ligand transport through the channel. I tried two SMDs (same pull rate, and force constant) with different starting structures (only ligand poses and position are slightly different). I performed the sampling of these two pathways, the plots obtained are of similar overall shapes, but peaks (max , min) have some variations? Could you please give your comment on this attempt? Is that expectable? Thank you, -- Aswathy -- Aswathy
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