Hi

I have force vs time graph and Pulling com positions vs time graphs and got from SMD simulations in gromacs the pulling velocity I am using is constant at 0.01 and the force constant was 1000 KJ/mol/nm, both plots are attached

I also performed the Umbrella sampling and the plot of the PMF is also attached with this question

I am interested in calculating kinetic off of the ligand protein binding for that I need rupture force vs loading rate plot, the slope ofthat graph tells the Kinetic off (Koff), the problem I am facing is that I am not sure how to calculate the loading rate in a simplest way through SMD simulations as I have seen many papers where loading rate is coming from AFM experiments.

The rupture force vs loading rate graph in the paper are fitted with bells - evans fitting but fitting the plot is second step first is to calculate the rupture force vs loading rate plot. Bells-Evans fitting is done in the following paper

Article Single molecule force spectroscopy data and BD- and MD simul...

Please can anyone help me in this analysis in a simplest way to get the rupture force vs loading rate through SMD simulations from the already attached plots with this question.

I will be really grateful to anyone who can help me in solving this issue.

Similar questions and discussions