Dear Axel and Steve
I’m making a data file using topotool, however, due to an unknown malfunction, an unrealistic bond appears in the data file.
I couldn’t fix that, so, I decided to set zero energy constant, i.e., Kb, for that bond (the bond style is harmonic).
Is it a correct? How can I ignore the effect of a redundant bond or angle without removing it?
Dear Axel and Steve
I’m making a data file using topotool, however, due to an unknown malfunction, an unrealistic bond appears in the data file.
I couldn’t fix that,
with topotools you can remove individual bonds.
so, I decided to set zero energy constant, i.e., Kb, for that bond (the bond style is harmonic).
Is it a correct?
no.
How can I ignore the effect of a redundant bond or angle without removing it?
you cannot. the presence of the bond will alter the neighbor list due to causing excluded pairs and you cannot have different exclusions settings for different bonds.
you must prepare a correct data file.
axel.