Bonds stretching across PBC for airebo

Hello,

I am trying to simulate a graphene sheet under uniaxial tension. While the simulation runs smoothly and the values I need are in agreement with literature (for most of the simulation), I see that when atoms cross the periodic boundary, the bond stretches across the sheet. I’ve looked up the mailing list for similar issues and I did come across some solutions involving ‘comm_modify,’ but as I understand, that is not necessary for a potential like Airebo. Can someone confirm that?

I have attached my input file, data file, and a vmd snapshot showing the bond stretch. Any ideas about how to fix this would be great.

Thank you

Vaidehi Menon

data.grn (15.3 KB)

in.gr_def (2.18 KB)

gr1png.png

Hello,

I am trying to simulate a graphene sheet under uniaxial tension. While the simulation runs smoothly and the values I need are in agreement with literature (for most of the simulation), I see that when atoms cross the periodic boundary, the bond stretches across the sheet. I’ve looked up the mailing list for similar issues and I did come across some solutions involving ‘comm_modify,’ but as I understand, that is not necessary for a potential like Airebo. Can someone confirm that?

I have attached my input file, data file, and a vmd snapshot showing the bond stretch. Any ideas about how to fix this would be great.

this is an artifact of the visualization. VMD will define bonds heuristically at the beginning of the trajectory and then assume they don’t change.
either you have to change your visualization in VMD (e.g. using the dynamic bonds representation) or use a different visualization software, that determines bonds differently and dynamically, or not visualize the bonds at all.

axel.