[gmx-users] Dummies usage doubts

Jones de Andrade johannesrs at gmail.com
Thu Oct 11 05:47:11 CEST 2007

Hi all.

Well, I'm having a bit of trouble here because the work has decided to go in
the direction of something I've never used before with gromacs: dummy atoms
(or now "virtual sites").

I've got at least three questions in order to use them:

1 - does the virtual sites need to be included in the .gro files in order to
make a simulation run?

2 - do I need to include them in the "exclusion list"?

3 - do I need to include them in the "atoms" section?

Thanks a lot in advance for any help anyone can provide in these subjects.

Sincerally yours,

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