Atoms on the other side of the box
Dear all, I am trying to minimize the volume of my Gromacs simulation box and therefore in some frames of the trajectory, the atoms appear on the other side of the box. Is there a way to correct this problem in ChimeraX or do I need to resolve it in Gromacs? Best Sasha
Hi Sasha, If you mean that parts of your main solute cross the periodic boundary during the trajectory, you would normally post-process your trajectory to rewrite it so that the main solute remains centered in the periodic box. For Gromacs, the program to do that and to keep other molecules together as they cross the boundary would be gmx trjconv. <https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html> If you mean that small molecules/solvent appear to "jump" across the periodic boundary during playback, you can use this ChimeraX Recipe <https://rbvi.github.io/chimerax-recipes/box_crossers/box_crossers.html> to select residues that cross the boundary during the trajectory. You could then easily hide them. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 13, 2025, at 2:38 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear all, I am trying to minimize the volume of my Gromacs simulation box and therefore in some frames of the trajectory, the atoms appear on the other side of the box. Is there a way to correct this problem in ChimeraX or do I need to resolve it in Gromacs? Best Sasha _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Eric, Thank you for the explanation. Everything works fine with gromacs. Thanks also for the recipe. Best Sasha From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Wednesday, May 14, 2025 00:32 To: Alexandra Zahradnikova Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Atoms on the other side of the box Hi Sasha, If you mean that parts of your main solute cross the periodic boundary during the trajectory, you would normally post-process your trajectory to rewrite it so that the main solute remains centered in the periodic box. For Gromacs, the program to do that and to keep other molecules together as they cross the boundary would be gmx trjconv. <https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html> If you mean that small molecules/solvent appear to "jump" across the periodic boundary during playback, you can use this ChimeraX Recipe <https://rbvi.github.io/chimerax-recipes/box_crossers/box_crossers.html> to select residues that cross the boundary during the trajectory. You could then easily hide them. --Eric Eric Pettersen UCSF Computer Graphics Lab On May 13, 2025, at 2:38 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear all, I am trying to minimize the volume of my Gromacs simulation box and therefore in some frames of the trajectory, the atoms appear on the other side of the box. Is there a way to correct this problem in ChimeraX or do I need to resolve it in Gromacs? Best Sasha _______________________________________________ ChimeraX-users mailing list -- <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users@cgl.ucsf.edu To unsubscribe send an email to <mailto:chimerax-users-leave@cgl.ucsf.edu> chimerax-users-leave@cgl.ucsf.edu Archives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Alexandra Zahradnikova -
Eric Pettersen