[gmx-users] (no subject)

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 29 09:11:43 CET 2004

On Mon, 2004-11-29 at 03:00 +0100, Marcin Wojdyr wrote:
> Hello,
> I'd like to simulate nanoparticles of ZnS (sphalerite) and I'm not sure   
>      how can I do it in Gromacs. I want to use Buckingham potential and   
>           harmonic angle potential for Zn-S-Zn bonds.
> Do I have to make a list of all Zn-S-Zn angles in particle?
> (I think I could treat a whole nanoparticle with >10^3 atoms as one
>  molecule and make a long lists of [atoms] and [angles]. But it's
>  rather not elegant. Can I do it in a simpler way?)
Use xyz2top to generate a topology (have to edit the ffgmx.n2t file) and
run with pbc=full (if it is crystalline)
> MW
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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