[gmx-developers] adding new atom types to gromacs "shell model"

David spoel at xray.bmc.uu.se
Wed May 5 10:14:03 CEST 2004

On Wed, 2004-05-05 at 02:36, Julius Su wrote:
> Hello,
> I had some questions about the shell model implemention in GROMACS --
> (1) is it possible to define new shell types?
Can you make yourself more clear? Right now a shell is a point charge
connected to another particle (or dummy position) with a spring. The
shell is massless and its position is optimised at every time step.
Obviously one can also give them a mass (e.g. 1 amu) and do normal

> (2) are the shells point charges or gaussian charges (screened coulomb
> interaction)?
Point charges. It is not very difficult to screen the Coulomb
interactions using table lookup, but then it becomes more difficult to
use PME for electrostatics.

> (3) is it possible to restrict the shells to interact with only a subset
> of atoms?
There is a mechanism called energy_exclusions where you list two group
that do not interact. It may be too simple for what you want

> Thanks,
> Julius
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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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