[gmx-users] Bond breakage modelling

[Ali Khodayari]

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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