[gmx-users] Transition metals topology

Matteo Busato busato.matteo at spes.uniud.it
Mon Jan 23 10:42:41 CET 2017

Good morning to everyone,

I am a new user of GROMACS and I'm trying to perform a very simple dynamics: a Nickel atom in a box with 1000 molecules of water. I got some troubles with the topology file and it is not totally clear to me how to treat transition metals on a topology level (knowing that metals are an 'exotic' subject in gromacs).

This is the very simple topology file I've tried to use, with OPLS force field and spce water on GROMACS 5.0.4:

; Topology for Nickel in SPCE

#include "oplsaa.ff/forcefield.itp"

; water topology

#include "oplsaa.ff/spce.itp"

;Ni topology

[ moleculetype]
; Name   nrexcl
ni     1

[ atoms ]
;id   at type   res   nr   residu name   at name   cg nr   charge   mass
1      ni      1LIG         NI            NI        1       2        58.69340

[ system ]
; Name
Nickel in water

[ molecules ]
; Compound             #mols
SOL                    1000
NI                       1

The problem of course consists in the fact that gromacs doesn't recognize any atom named as 'ni' because it doesn't have it in its libraries.

The question is: due the fact that I possess the proper Lennard-Jones parameters downloaded from the literature for Ni (parameters that I had not included in this topology-just because the program did not recognise them), what should I do to make gromacs recognise this species? Should I add 'ni' with its parameters in the atomtype file of the library of the forcefield and the L-J parameters in the non-bonded interaction file?

Thank you in advance for your answers, and I apologyse if I wrote something unsophisticated, but I am a gromacs user since a couple of months. Thank you.

Kind regards, Matteo Busato

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