GROMACS version:
GROMACS modification: Yes/No
Here post your question I have done ligand pulling from protein. and got this umbrella . can please anytell is my graphs correct of wham and pmf. or do i need to correct my sampling window or anything else. (pfa)
Please, don’t start multiple threads with the same questions (Interpretation of wham and pmf).
You seem to have a reasonable umbrella overlap, I think that is about as much as can be said about the output. I would perhaps consider adding more umbrella windows at approximately 0.95, 1.6, 1.9 and 4.55, since the overlap there is quite limited.
Regarding the PMF, it’s not possible to say if it’s correct or not. You are the domain expert. Does it look good to you? What are the error estimates? When doing the analysis, does the PMF look the same if you discard the first 1/2 of the data? The last 1/4? Otherwise, that may be an indication (but far from a fool-proof test) that you need to increase your simulation time.