[gmx-users] indexing atoms
toma0052 at umn.edu
Thu Nov 30 05:44:19 CET 2006
I am wondering about a response I got a while ago about indexing
atoms. I am not very familiar with awk, but it seems like a fairly simple
way to search through a .gro file and find the solvent molecules with a
particular z-coordinate range, as I need for my simulation. My question
however, concerns implementing this into an md run. I would like to add
an acceleration to solvent molecules that are within a certain distance
from a lipid bilayer. However, if the solvent molecules diffuse too far
away during the md run, I no longer want them to have an acceleration.
Therefore, it appears that at every time step I need to perform a check to
see which solvent molecules are close enough to warrant an acceleration.
So, is there a way that I can incorporate the awk file such that it runs
and creates a particular index group at every time step? If not, is there
some other way that I can check at each time step (or every several time
steps) which solvent molecules have a particular z-coordinate and give them
On 31 Oct 2006, Erik Marklund wrote:
> 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=3D[4 5] nm and remove everything
> except the indexes. Put a bracketed name on top of it all and
> 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
> > 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
> > the solvent, but not the entire solvent. Is there a way that I can
> > solvent molecules within a certain coordinate ie. a z-position from
> > 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
> > keep its fixed acceleration. Is there any way that indexing by
> > 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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