[gmx-users] Transition metals topology

Mark Abraham mark.j.abraham at gmail.com
Mon Jan 23 15:48:02 CET 2017


A good form for the solution depends whether these Ni parameters are
supposed to work with any force field (or water model). (If none, then you
have a bigger problem...) You can copy the whole forcefield folder from
$gromacsinstall/share/top into your working directory and edit the
[atomtypes] and/or [nonbond_params] sections to add support for this atom
type. Chapter 5 of the reference manual is your friend for understanding
how that all works.

Or if you just want Ni and water, then you can forget about the force field
libraries and write your own single-file .top that does everything. You'll
still need to declare how you want all the details to work, as the normal
force fields do, which are all described in those same docs.


On Mon, Jan 23, 2017 at 10:43 AM Matteo Busato <busato.matteo at spes.uniud.it>

> 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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list