[gmx-users] FCC cell
Mark.Abraham at anu.edu.au
Wed Feb 7 01:05:29 CET 2007
Eudes Fileti wrote:
> Dear David
> I did just as you and Mark Abraham had suggested. I
> have made the unit cell using another software and I am
> already to use PBC. However a doubt appeared. As there are 840 atoms
> in the unit cell (is a fullerene crystal), how can I generate the top file?
You could do it directly with pdb2gmx but you may run into problems
depending on the formatting of your existing structure file.
> Must I make an file top with all these atoms and its parameters (of
> potential and geometric)?
> Or there is another way to make it, using for example, only a site of
> the lattice
> (in this case a C60 fullerene)?
Yes, you can have multiple copies of the same molecule with the same
topology by following the methodology of manual section 5.6.2. The
easiest way to generate the molecule.itp file in the first place is to
start with a single-molecule structure file, feed that to pdb2gmx, hack
the output .top file to .itp format by hand and make a new .top file for
your real system.
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