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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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