[gmx-users] dummies...confused

[Anton Feenstra]

Senthil Kandasamy wrote:
> I do not understand the negative values for the "funct" variable.

A trick to invert the chirality. Not sure if it is actually documented.
(Doesn't necessarily work for all interaction functions.)

> Also,is the first column in the dummies directive is the atom number of
> the dummy to be constructed (with the atomname e.g. MNH3), or is it the
> atom number of the hydrogen atoms beng dummyfied? 

The dummy to be constructed, which is in this case the hydrogen atom.
The MNH3 is not a dummy atom in this terminology, but a 'Dummy Mass',
it doesn't correspond to any physical atom.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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