Thank you Peter, I will try to have a detailed look.
Regards, Ali
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Peter Kroon
Sent: dinsdag 19 februari 2019 13:41
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Bond breakage
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
GROMOS or
else.
Kind regards,
Ali
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Paul Bauer
Sent: dinsdag 19 februari 2019 13:43
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Bond breakage modelling
Hello,
in general I would advise not to use
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
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 wrote:
>
> Hi Ali,
>
>
> The short answer is "not
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
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
