[AMBER] Bond breakage modelling

From: Ali Khodayari <ali.khodayari.student.kuleuven.be>
Date: Wed, 20 Feb 2019 14:04:13 +0100

Dear All,


We have simulated a cellulose fiber using GLYCAM06 parameter set. The model
is simulated in GROMACS (after conversion through acpype) 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 Amber neglect
bonds from a certain cut-off onwards? Of course I am not an Amber expert,
but it will be very helpful if we can perform the simulations in Amber.


Thank you in advanced for your responses.

Kind regards,



AMBER mailing list
Received on Wed Feb 20 2019 - 05:30:03 PST
Custom Search