[gmx-users] generating Topology file of Metal Oxide

[André Farias de Moura]

It is doable, we have just finished a study (not published yet) of TiO2
nanoparticles oriented attachment.

But like Justin told you, GROMACS does not have any native support for that
kind of system, so you're on your own to build topologies and to extract
information from the trajectories (GROMACS has no built-in analysis tool
for crystalline solids whatsoever, although you might use some general
analysis like rdf/densities, electrostatic potential, etc.)

Andre

On Wed, Feb 28, 2018 at 10:04 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/28/18 7:14 AM, Kanwal Gill wrote:
>
>> Respected sir/ madam,
>>
>> I start MD silmulations with metal oxides but failed to generate its
>> topology file. i also checked with diferent softwares like PRODRG or ATB,
>> but do not get the topology file. please suggest me the solution.
>>
>
> GROMACS probably isn't the best software for such systems (you could make
> it work, but it would be pretty painful), and the built-in biomolecular
> force fields were definitely not designed to handle metal oxides, so it's
> no surprise that programs that generate GROMOS topologies would have failed.
>
> -Justin
>
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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