Hello everyone

Can anyone please help me on how to calculate PMF of my SMD (Steered molecular dynamics) data without performing umbrella sampling… Is it possible to calculate PMF with **gmx wham**, if umbrella sampling is not performed…

Generating a PMF from WHAM requires umbrella sampling. You can’t perform one SMD (non-equilibrium) simulation and generate a PMF.

Okk sir… Can you please suggest other method to calculate PMF using SMD data…

I have already plotted Force-extension curve, now How should I proceed towards PMF…

The Jarzynski method can be used in non-equilibrium simulations, but it requires running a great many SMD calculations along different paths and honestly is no faster/cheaper than doing umbrella sampling. To compute a PMF, it is unavoidable to perform the umbrella sampling simulations in this context.

Sir… Can you please help me in knowing… What data is exactly required for plotting the PMF of non-equilibrium simulations… I have already plotted force-extension curve but now I am stuck there… How should I proceed?