Hello Prof. Dubbeldam,
I would like to use TraPPE – Explicit Hydrogen model to define a flexible di-n-propylamine molecule. For TraPPE-EH alkane models interaction sites for hydrogen are shifted from the atomic nuclei out to the C-H bond center. I would like to ask how can I set dummies in a molecule definition file?
Kind regards,
Ivan
Either use a model that puts the charge-centers on the atomic centers (OPLS) or if the molecule is small you can also make the whole molecule rigid.