[gmx-users] Trajectories

Peter C. Lai pcl at uab.edu
Tue Jun 5 22:23:15 CEST 2012

You can also use something like VMD where you load the trajectory then 
select your atoms, then increment the frames and extract the xyz coordinates
of each of your atoms in the selection. You can do that in 5 lines of TCL
script (just don't update the select within selection after each frame or
else it will reselect a new set of molecules based on the distance criteria,
if you're trying to track the same water molecules from beginning to end).

On 2012-06-05 06:02:22AM -0700, rankinb wrote:
> I am interested in pulling out the trajectories (x,y,z coordinates) of water
> molecules within a certain distance of my solute molecule.  I have tried
> using g_select, but that will only give me the atom numbers and not the
> trajectories.  I can create an index file using this command but
> unfortunately each time frame is set as a different group.  
> Is there a way to get the trajectories at all frames of only the water
> molecules within a specified distance of a solute molecule? 
> Thank you very much,
> Blake
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Peter C. Lai			| University of Alabama-Birmingham
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