[gmx-users] force field parameters for Fe3O4?

[rose rahmani]

Hello,

I use AMBER force field.
So, how about periodic structures? like inorganic nanosheet and nanotubes?

Thank you so much

On Fri, 13 Apr 2018, 14:50 Paul bauer, <paul.bauer.q at gmail.com> wrote:

> Hello,
>
> this depends on the force field you are using. Some of them use
> parameters from a QM optimization and partial charge calculation.
> But even then you need to be careful that the results from the QM are
> not just random numbers :)
>
> But I'm not sure myself how I would tackle something like Magnetite
> right now, as it would also require obtaining parameters for the LJ
> interactions.
>
> Cheers!
>
> On 13/04/18 12:13, rose rahmani wrote:
> > On Fri, 13 Apr 2018, 14:35 Paul bauer, <paul.bauer.q at gmail.com> wrote:
> >
> >> Hello,
> >>
> >> I would recommend that you check relevant publications for the
> >> simulation of magnetite if people have tried to simulate it in solvent.
> >> I could not find anything during a short search, but maybe you'll be
> >> more successful. :)
> >> If there are no published parameters in the literature you will have to
> >> parametrize the molecule yourself according to the method used by the
> >> force field you are using.
> >> I would look at the section in the user guide dealing with this
> >> (
> >>
> http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields
> )
> >>
> >>
> > Is it true to optimize the molecule for example in gaussian(dft)first,
> and
> > then calculate the charges and make an .itp file for it?is it always
> > reliable?
> >
> >> and then at the documentation for your force field!
> >>
> >> Cheers!
> >>
> >> On 13/04/18 11:21, leila karami wrote:
> >>> Dear gromacs users,
> >>>
> >>> I want to simulate a protein in different concentration of Fe3O4.
> >>>
> >>> How to obtain force field parameters of Fe3O4?
> >>>
> >>> Any help will highly be appreciated.
> >>>
> >>> Best,
> >>
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