I'm trying to calculate the PMF of the distance between the C-terminal and N-terminal of a protein after performing umbrella sampling simulations where I pulled the protein apart. I ran simulations, each with a harmonic restraint to sample different distances between the C-term and N-term.
And then I've modified the example/umbrella-sampling-fes/umbrella-sampling.py script to fit my data, but I'm encountering an error that I'm not able to diagnose as below
Could someone help me understand what might be causing this error?
Attached is the time series data files from simulation and my python script.
Hello,
I'm trying to calculate the PMF of the distance between the C-terminal and N-terminal of a protein after performing umbrella sampling simulations where I pulled the protein apart. I ran simulations, each with a harmonic restraint to sample different distances between the C-term and N-term.
And then I've modified the
example/umbrella-sampling-fes/umbrella-sampling.pyscript to fit my data, but I'm encountering an error that I'm not able to diagnose as belowCould someone help me understand what might be causing this error?
Attached is the time series data files from simulation and my python script.
pymbar_us
Best regards,
Jinyoung