[gmx-users] How to orientationally restrain a molecule?

Michael Shirts mrshirts at gmail.com
Mon Apr 24 22:50:48 CEST 2017

I'm interested carrying out a long simulation of a thin, narrow protein.
Clearly, the volume-minimizing way to do this would be to put it in a thin,
narrow box of solvent.  The issue with this is that it could rotate around
and interact with itself. if the orientation of the protein changed
relative to the orientation of the box.

Is there a good way to restrain the orientation in GROMACS currently?  I
looked a little at the orientation restraint for NMR, but it didn't seem
like that would really work well (or at least, it was not obvious it would
work well), for restraining the overall orientation.  Am I missing

Any other thoughts, suggestions for doing this?  Has anyone else done this?


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