From: Vermaas, Joshua (
Date: Thu Aug 15 2019 - 15:56:09 CDT

Hi Alex,

Have you tried wraping first, and then doing the alignment? What I suspect happened is that your water box becomes tilted when you align your protein, and then the rather simpleminded moves along the three axes that the wrapping command does do not taken this tilted periodic box into account, and so you get incorrect atom positions.


On 2019-08-15 14:46:40-06:00 wrote:


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

The trajectory Im 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 Im using to measure distances between two atoms is measure bond {i j}, where i and j are the indices of the atoms Im interested in.