Unreasonable results with gmx wham

[sallaprat]

GROMACS version: 2022.4
GROMACS modification: No

Dear all,

I am running gmx wham with the following command: gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal

My results are not reasonable and dramatically change with the binning and the amount of sampling. This is the window overlap:

When computing the FES, I obtained the black line with half of the sampling (I only run half of the windows) and that PMF makes sense for my system. However, using all the sampling, the profiles is basically a flat line. I have been playing with the binning and with 60 bins I get the results below. I obtained the orange line with 100% of my windows and the blue line with the 90% of my windows. You can see that the profile is really different.

Could you give me some advice on how to fix this?

Thank you very much,

Sara

[therealchrisneale]

at the very least, you have some regions with no sampling overlap. In the absence of sampling overlap, I’m not even sure what wham results mean. I’m also unclear why you would start removing umbrellas.