[gmx-users] Bond breakage modelling

Paul Bauer paul.bauer.q at gmail.com
Tue Feb 19 13:43:30 CET 2019


in general I would advise not to use a classical force field to model a 
quantum mechanical effect like breaking a bond.
Classical force fields are not parametrized to reproduce those effects, 
and while you might get something that looks fine with the morse 
potential it would definitely be unphysical.
If you want to study quantum effects, use a QM method for the parts that 
are involved in bond breaking, or use a reactive force field like ReaxFF.



On 2019-02-19 13:35, Ali Khodayari wrote:
> Dear Peter,
> Thank you for your prompt reply.
> I think I can try the morse potential to see how the system responds.
> Could you kindly provide some more info about how to implement it?
> Best regards,
> Ali
>> On 19 Feb 2019, at 11:35, Peter Kroon<p.c.kroon at rug.nl>  wrote:
>> 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.
>> Peter
>>> 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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