[gmx-users] how to define the dummy atoms in gromacs

Jochen Hub jhub at gwdg.de
Tue Mar 31 09:31:40 CEST 2009

He, Yang wrote:
> Hi all users,
> I need to add some dummy atoms in my case. I know that I need to include the section [virtual_sites] in the top file but I am not sure how to define them in the itp file .Do I need to list these atoms in the section[atoms] ? Can anyone of you give me some suggestions about that?

Define them in the atoms section and list them as dummies in the dummie
section. Check the manual for detail.


> Thank you in advance.
> Yang
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Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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