Hi,
I am working with a spherical structure and need to calculate the PMF for my drug within this sphere using umbrella sampling. However, I am encountering an issue where the sphere moves within the simulation box.
What settings should I adjust in the MDP file to ensure the sphere remains fixed during the simulation? I am concerned that applying a total pulling force or position restraints might affect the PMF results.
I would really appreciate any guidance on this. Thanks in advance!
Best regards,
Shiva Najafian