[gmx-users] Bond breakage modelling

Peter Kroon p.c.kroon at rug.nl
Tue Feb 19 12:04:54 CET 2019

Hi Ali,

The short answer is "not really". You could model your bonds as
non-bonded (morse) potentials, but then you lose all angle dependence on
the potential energy, since the non-bonded potentials must be pair-wise.
Depending on the exact problem this may be acceptable though. The angle
dependence on the potential energy also immediately points out an issue
with your cut-off based approach: how will you deal with the angle(s)?

In literature I have seen some papers of people pulling proteins apart,
breaking cystein bridges. Those may contain some insight/ideas.


On 19-02-19 11:28, Ali Khodayari wrote:
> 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,
> Ali

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