Niamh Jimenez

2 Questions 1 Answers 0 Followers

Questions related from Niamh Jimenez

UMBRELLA SAMPLING: How can I calculate dG from a PMF curve in automated fashion?

1. I am processing my umbrella sampling simulations using the Weighted Histogram Analysis Method in Gromacs (gmx wham). However, I would like to report the mean dG and a standard deviation. To do...

16 March 2020 1,589 3 View

How do I calculate free energy of binding for ligand-protein complex using Bennett Acceptance Ratio (BAR)?

Hi, I am familiar with performing MD simulations using Gromacs on protein-ligand complexes. However, BAR is a new technique to me and I need specific clarification of the decoupling sequence...

13 March 2020 3,750 1 View