[gmx-users] force field parameters for Fe3O4?

Paul bauer paul.bauer.q at gmail.com
Fri Apr 13 12:20:40 CEST 2018


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 


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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