[gmx-users] Bond breakage modelling

Ali Khodayari ali.khodayari at student.kuleuven.be
Tue Feb 19 11:28:56 CET 2019

Dear All,


We have simulated a cellulose fiber using GLYCAM06 ff parameters converted
to GROMACS. The model is validated and works properly.  

We are investigating the behavior of the material under tensile load.
However, as covalent bonds are modelled with a harmonic potential -as it is
in most of the non-reactive force fields- some parameters cannot be
extracted. Is there any way to mimic the breakage of the bonds, let's say
when the distance of the atoms exceed a certain amount? In other words, if
we have a rough idea of the strain at which bonds break, can GROMACS neglect
bonds from a certain cut-off onwards?

Thank you in advanced for your responses.

Kind regards,


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