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?