[gmx-users] indexing atoms

Erik Marklund erikm at xray.bmc.uu.se
Tue Oct 31 09:39:01 CET 2006

You can sort the atoms according to position using grompp, but I don't
think that's the easiest solution. I would use awk or something along
those lines, to find all atoms within z=[4 5] nm and remove everything
except the indexes. Put a bracketed name on top of it all and violà, you
have turned them into an index group.


On Tue, 2006-10-31 at 00:37 -0600, toma0052 wrote:
> Hello,
>      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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Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se

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