[gmx-users] Bond breakage modelling

[Ali Khodayari]

Dear Paul,

Thank you for your response. Unfortunately, ReaxFF shows some discrepancies
in some cases when it comes to carbohydrates. Besides, its parameters are
not written for GROMACS. I am looking for maybe a code to mimic this
behavior using the validated force fields for carbohydrates, say GROMOS or
else. 

Kind regards,
Ali

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Paul Bauer
Sent: dinsdag 19 februari 2019 13:43
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Bond breakage modelling

Hello,

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.

Cheers

Paul

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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