GROMACS version: 2018
GROMACS modification: No
Dear GMX users,
I performed two umbrella sampling simulations of interaction of two short peptides for 20 ns each window. I got some weird PMF figures as I attached. It means that there are sharp curves for both simulations. How can I get smooth PMF?
Second, the converged values of these PMF is around -3 kcal/mol. How reliable are these curves?
Best regards,
Batsaikhan
Look at the histograms. You probably have a few regions of poor sampling/poor overlap.
Dear prof. Justin,
Thank you very much for your prompt reply. I attached one of the histograms. It looks much overlapped. Should I increase simulation time of the windows.
Best regards,
Batsaikhan
You have way too many windows that are almost redundant. There is really uneven spacing across the reaction coordinate. You need to refine your window spacing, force constants, or both. And you may still need more sampling time after you do that.
Dear prof. Justin,
Thank you very much for your clear explanation.
Best regards,
Batsaikhan
Dear prof. Justin,
Hello, thank you for your time.
I performed umbrella sampling simulations for dimer structure of a short peptide.
When I perform WHAM analysis, the histogram is good enough as following. However, the PMF plot is weird. How can I get good PMF curve? Please advice me.
Best regards,
Batsaikhan
Looks fine to me. What do you think is the problem?
Dear prof. Justin,
Thank you very much for your reply. I have tried many times to get this kind of histograms using different forces and different simulation times. Some of calculations showed the higher converging values in profile plot around 1 or 2 kcal/mol. However I used very strong pulling force, I observed uneven distributions in strong pulling simulations.
Therefore, I expected that the profile curve should be converged around positive E values.
Thank you very much again.
Best regards,
Batsaikhan
pls how can i run PMF at gromacs
Please can I have the PMF script to run it on gromacs and thank you.
Hello dear professor. I have performed an MD simulation for 200 ns, and now I’m wondering if there is a script that I can use for HPC to calculate the potential of mean force (PMF) using umbrella sampling. Thank you.
Dear jalemkul,
How do I need to enhance sampling in regions with poor sampling along the reaction coordinate? In my work, I run 180 simulations of 100 ns (umbrella sampling) to represent the translocation process of a polymer through a membrane. The umbrella histograms shows a poor sampling around 4 nm:
I tried to run more simulations, but they did not sample the region around 4 nm.
You need more windows to fill the gap, perhaps with a stronger force constant if it is a very high-energy region of the reaction coordinate.
