From: Alex Hummels (
Date: Thu Aug 15 2019 - 14:42:02 CDT


I have been trying to identify water molecules that are a certain distance from a protein. However I’m getting some distances that are extremely weird (for example an O in the protein backbone is measured as 0.20 Å away from an OH2 molecule at one time step - they’re practically on top of each other).

The trajectory I’m looking at was initially run as unwrapped, but I am interested in measuring distances when the trajectory is wrapped. To wrap the trajectory, after loading in the .psf and .dcd files and aligning the protein backbone to the first frame, I performed the following command

pbc wrap -all -compounds res -center com -centersel protein -sel water

Does anyone have any idea why certain atoms would be getting so close to each other?

For clarity, the command I’m using to measure distances between two atoms is measure bond {i j}, where i and j are the indices of the atoms I’m interested in.