[gmx-users] Trajectories

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================