[gmx-users] generating Topology file of Metal Oxide

Justin Lemkul jalemkul at vt.edu
Wed Feb 28 14:04:34 CET 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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