[gmx-users] indexing atoms

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 30 06:14:48 CET 2006

toma0052 wrote:
> Hello,
>      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
> an acceleration?

I presume you've read the relevant manual sections. If there's nothing 
useful there, the only way to do something like this would be to get 
inside the C code, loop over all solvent molecules after do_force to 
check for their position, and then adjust the force on them accordingly.


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