[gmx-users] indexing atoms

toma0052 toma0052 at umn.edu
Tue Oct 31 07:37:41 CET 2006

     I have a question regarding indexing atoms for use with
non-equilibrium MD.  The manual says that I can select atoms by number or
type; I was wondering if there is a way in Gromacs to index atoms by
position with the simulation box.  I am looking to add an acceleration to
the solvent, but not the entire solvent.  Is there a way that I can specify
solvent molecules within a certain coordinate ie. a z-position from 4nm to
5nm with the simulation box being 6nm in height?  I am looking to
accelerate solvent molecules near a lipid bilayer, but if a particular
solvent molecule diffuses too far from the bilayer, I no longer want it to
keep its fixed acceleration.  Is there any way that indexing by coordinates
is possible?

Thank you,
Mike Tomasini

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