[gmx-users] DUMMY and CONSTRAINED

Berk Hess gmx3 at hotmail.com
Wed Apr 21 14:47:01 CEST 2004

>I would like to performe a all-bonds constrain molecular dynamics, (I think 
>  shake) but I have dummy atoms in my sistems and I must define bonds 
>these dummy atoms.

Shake or lincs does not make much of a difference.

Dummies are not allowed to have constraints.
Their positions are a functions of the coordinates of the normal atoms.
Theoretically one could add constraints to dummies, but this would be
quite complicated to implement as one should not move the dummy,
but the atoms that it is constructed from.

I saw that your two dummies both have six constraints.
In that case you could just use normal particles instead of dummies
and the dynamics would be almost identical.


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