[gmx-users] huge center of mass distance mismatch in umbrella sampling

Irem Altan irem.altan at duke.edu
Mon Jan 22 00:53:46 CET 2018


I have two copies of a protein that are in contact with each other. Their center of mass distance is about 5.5 nm. However, in the resulting potential of mean force, there is an energetic minimum at 3.5 nm. How is this at all possible? At that distance half of the protein would be overlapping each other. How could I diagnose why this is happening?



More information about the gromacs.org_gmx-users mailing list