[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:
> 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)
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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