[gmx-users] MD for inorganic compound

André Farias de Moura moura at ufscar.br
Tue Mar 28 19:44:51 CEST 2017

Fixed charges may work as well, although some parameterization might be

there are plenty of papers reporting such simulations, for instance:

Langmuir, 2015, 31 (48), pp 13127–13137
*DOI: *10.1021/acs.langmuir.5b03167

On Tue, Mar 28, 2017 at 2:27 PM, Michael Brunsteiner <mbx0009 at yahoo.com>

> > Anjali Patel wrote:> What is the procedure of using gromacs specially
> for inorganic compound??> I am beginner for gromacs simulation package, I
> used it for organic
> > compounds. But unable to understand how to deal with inorganic compounds
> > and what about the force field and solvent we can use.
> as Justin wrote, you can use gromacs to model any material on the
> molecular scaleas long as you have a decent force field.This being said:
> gromacs was originally built primarily with (bio-)organiccompounds in mind,
> and here the fixed partial charge model that is defaultin gromacs is good
> enough in many cases. When you deal with inorganic compoundsespecially with
> salts and/or materials in the solid state accounting for polarizability
> mightbe essential for getting good results. In this case you have two
> choices:
> 1) stick with gromacs and use the shell model. Here its worthwhile looking
> at the   work of Richard Catlow and co-workers. they did a lot of work in
> this field - however,
>   be careful here as published shell-model force fields are in most cases
> not widely tested  compared to the commonly used fixed charge force fields.
> 2) turn to DFT/plain wave basis set models and software
>    (see https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_
> solid-state_physics_software)
> cheers,
> Michael
> > With regards
> > Anjali Patel
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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