[gmx-users] Trajectories

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 5 15:05:09 CEST 2012

On 6/5/12 9:02 AM, 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?

At present, there is no elegant way to construct such a trajectory, since, in 
principle, each frame can have a different number of atoms based on which water 
molecules satisfy the given criteria.  Each index group that g_select provides 
corresponds to an individual frame in the original trajectory, which you can use 
to pull out individual coordinate files.  Perhaps a multi-frame .pdb or .gro 
file would work, but I believe that .xtc and .trr files have to have the same 
number of atoms in each frame to be interpreted correctly.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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