[gmx-users] Bond breakage modelling

[Ali Khodayari]

Thank you Peter, I will try to have a detailed look. 
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 Peter Kroon
Sent: dinsdag 19 februari 2019 13:41
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Bond breakage modelling

I've never done it myself, so not really. The manual should help :)

I don't know if Morse potentials come built-in, or that you'll need to make
tables.

Be aware that if you have three or more morse potential particles together
they can and will form stable triangles, because there is no influence of
the angle on the potential.


Peter

On 19-02-19 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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