[gmx-users] Creating metal ion dummy models for MD simulations.

Abhishek Acharya abhi117acharya at gmail.com
Tue Jul 25 10:40:21 CEST 2017

Dear Users,

I want simulate a protein bound to two copper ions. For this, I intend to
use a dummy model for the metal ions with 6 dummy atoms surrounding each
metal ion. The parameters will be obtained from the following publication:


Since, I am new to the use of dummy models in GROMACS, I wanted to know the
correct way to represent the topology for such models. I tried to look for
example .itp files but couldn't find one. I went though the gromacs manual,
especially dummy atoms section (or virtual sites). But, I am pretty sure
this is not applicable to my problem; virtual sites have no mass, whereas
the dummy models as described in the above publication have dummy atoms
with a mass of 3.000 amu. I am guessing that the correct way should be to
treat the dummy model as a single molecule with 7 atoms, one central metal
ion and 6 dummy atoms, but i may be wrong.

Kindly let me know the correct method to represent the topology.
Alternatively, it would also be a great help if someone can provide itp
files used in the above study, or any example itp files with similar dummy

Also, which software is generally used to construct the coordinates for
such dummy models ?

Thanks and Regards,

Abhishek Acharya
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,

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