[gmx-users] Topology file for diamond nanocrystal in water

David spoel at xray.bmc.uu.se
Tue Oct 4 20:38:30 CEST 2005

On Tue, 2005-10-04 at 21:36 +0400, Гена Ионов wrote:
> Hello!
> I tried to convert pdb file with small diamond (about 200 atoms of C) into
> *.gro and *.top file, but problem in building topology file for 3D net
> of bonds in diamond crystall. System not infinite, have water shell
> and periodic bonds not appropriate.
> Haw I can build such topology file? May be it take into account all 200 atoms?
> But then may be exist any software for this automatic generation
> topology files for covalent crystal?
try prodrg server or the x2top program.

> Many thanks for any advice.
> Gennady V. Ionov.
> gionov at mail.ru
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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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