[gmx-users] intermolecular distance restraint

Jochen Hub jhub at gwdg.de
Tue Apr 14 12:59:21 CEST 2009

Hi Warren,

if you want to use distance restraints, the two proteins must be in the
same gromacs "molecule". AFAIK, it is impossible to use distance
restraints between atoms of different molecules. Altermatively, you may
want to consider bonds of type 6 (not subject to lincs).

pdb2gmx -merge is useful to create the topology of a "molecule" that
actually contains 2 proteins.

If the two proteins must be in different gromacs "molecules", you would
have to use the pull code.


warren deng wrote:
> Hi Gromacs users,
> In my simulation, I need to restrain distances between atoms on two protein
> molecules. But the Gromacs manual on NOE seems to imply that the atom
> indices belong to the same molecule type.
> So I am wondering whether it is possible to create distance restraint
> between two molecule types in Gromacs?
> Many thanks,
> Warren
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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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