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