[gmx-users] nanoparticles (was: no subject)
spoel at xray.bmc.uu.se
Wed Dec 1 19:37:26 CET 2004
On Wed, 2004-12-01 at 19:11 +0100, Marcin Wojdyr wrote:
> On Mon, 29 Nov 2004, David van der Spoel wrote:
> > 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?)
> > No.
> > Use xyz2top to generate a topology (have to edit the ffgmx.n2t file) and
> > run with pbc=full (if it is crystalline)
> When I run x2top I get [bonds], [angles] and [dihedrals].
> What can I do if the only bonded interactions I'd like to use is harmonic
> angle potential? (I mean is there a more elegant solution than
> just removing [bonds] and [dihedrals] from topology file?)
Not implemented. How do you treat Zn-S interactions then?
> BTW I searched for description of x2top and noticed that in manual-3.2.pdf
> there is section E.148 called "x2top" and E.149 called "x2top_d". Both
> are the same. Actually all manual pages are duplicated. I tried to find
> out how this manual is generated, but I haven't found anything in CVS
OK, silly error.
> BTW2 I tried to compile Gromacs with -DDEBUG, but it fails (there are some
> bugs in #ifdef DEBUG / #endif sections).
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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