[gmx-users] intermolecular distance restraint

[warren deng]

Hi Jochen,

Thanks a lot for the information, I appreciate. I will merge the two
proteins into a single moleculetype and apply the distance restraint, as you
suggested. Although I could try use the pull code, I am not sure if they
interfere with free energ (lambda) code which I am also using.

With best wishes,

Warren

On Tue, Apr 14, 2009 at 6:59 PM, Jochen Hub <jhub at gwdg.de> wrote:

> 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.
>
> Best,
> Jochen
>
>
> 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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