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 [email protected].
