From: Jérôme Hénin (
Date: Thu Aug 15 2019 - 16:06:53 CDT

Hi Alex,

you need to wrap first and align second. The alignement rotates atomic
coordinates with respect to the PBC basis vectors, which then become


On Thu, 15 Aug 2019 at 22:23, Alex Hummels <> wrote:

> Hello,
> 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.
> Thanks,
> Alex