[gmx-users] Non-bonded Copper

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jun 29 08:40:37 CEST 2009

Hi Matthew,

On top of the advice of Mark, consider that Copper has a rather
peculiar electronic structure, which may make it difficult to model
using only a Lennard-Jones potential for the non-bonded interactions.
And then it will also matter whether it's Cu(I) or Cu(II). Are you
sure that the simple approach you try to take is suitable to give a
good enough answer to the issue you want to address?



On Mon, Jun 29, 2009 at 1:45 AM, Mark Abraham<Mark.Abraham at anu.edu.au> wrote:
> Matthew Roode wrote:
>> Greetings all,
>> Let me preface this by stating I'm new at MD simulation.  I am trying to
>> perform a simulation which involves non-bonded copper atoms, amongst other
>> things.  I'm making use of the Lennard-Jones potential to describe the
>> non-bonded interactions between them, and I've input the parameters in the
>> ff*nb.itp file after ensuring Cu was defined in the ffgmx.atp file.  I use
>> x2top to generate the topology file, but the program stops on a fatal error
>> telling me "No forcefield type for atom Cu (841) with 0 bonds".  Can any of
>> you out there offer any advice on the cause of said error?  Thus far my
>> troubleshooting has failed.
> As a general rule, don't use ffgmx. Like it says in the manual and pdb2gmx,
> its usage is deprecated.
> What you need is a forcefield that models non-bonded copper. That's easier
> said than found. Most forcefields in common use with GROMACS are for
> biochemical simulations, so you may not find anything suitable already in
> GROMACS. Telling us your whole simulation system would have been a good
> idea. Likely, you'll need to search literature for a suitable model, which
> GROMACS is likely to be able to implement. That might require a thorough
> knowledge of chapter 5 of the manual.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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