Hi Ben, Typically, one “wraps” a PBC trajectory to produce a new trajectory where molecules stay whole on one side of the box or the other. For Gromacs, the tool for that is trjconv, perhaps with the “-pbc whole” flags. See this page: gmx trjconv — GROMACS 2018 documentation <http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html>. If wrapping a trajectory is problematic for some reason, you could define a per-frame Python script to hide long bonds. I have attached such a script. To use it, in the MD Movie GUI choose the Per-Frame→Define script… menu entry, and in the resulting dialog change the script type to “Python” and use the “Insert text file” button near the button to insert the attached Python file. Then click OK. Long bonds should disappear and you can play your trajectory and bonds will be hidden and shown appropriately. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2020, at 9:10 PM, benjamintam <benjamintam@um.edu.mo> wrote:
Dear all,
I am a new user of Chimera, I have generate a .gro file from gromacs and put it into the chimera. However, the imagine has a lot of cross bonding due to the protein is crossing the PBC. Hence I would like to ask how to fix that so the imagine does not cross the pbc box.
Best regards,
Ben
Ph.D, M.Eng, FHEA
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