[gmx-users] nanoparticles (was: no subject)

Marcin Wojdyr wojdyr at unipress.waw.pl
Wed Dec 1 19:11:36 CET 2004

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?)

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

BTW2 I tried to compile Gromacs with -DDEBUG, but it fails (there are some
bugs in #ifdef DEBUG / #endif sections).

Marcin Wojdyr                       http://www.unipress.waw.pl/~wojdyr/

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