normal Umbrella Sampling to calculate PMF

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3 months 2 weeks ago #8126 by Sherryhan
Umbrella Sampling to calculate PMF was created by Sherryhan
Dear Martini-User,
I am trying to calculate the PMF between protein and nanoparticles by umbrella sampling. I have followed the Gromacs tutorials( www.mdtutorials.com/gmx/umbrella/05_pull.html ) to pull the nanoparticle. However, I am not sure about the pull_coord1_rate and pull_coord1_k. How can I choose a fit parameter for my system?
Thank you for your kind attention and looking forward to your reply.
Best regards,
Sherry

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3 months 2 weeks ago #8130 by bart
Replied by bart on topic Umbrella Sampling to calculate PMF
It depends on how hard you want to pull and how much it is allowed to deviate from that target. Higher numbers are stronger pulling and more stringent to the target force/rate. How hard you want to pull depends on your design choises. Usually if the system explodes you pull too hard, anything under that is a choice. If your pulling force/rate is in the thermal noise you could start calling it reversible, anything higher is out of equilibrium pulling, which might be what you want.

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