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