erikm at xray.bmc.uu.se
Wed Jun 6 10:15:27 CEST 2012
Pymol has similar functionality, in case you prefer that over VMD.
5 jun 2012 kl. 22.23 skrev Peter C. Lai:
> 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,
>> View this message in context: http://gromacs.5086.n6.nabble.com/Trajectories-tp4998094.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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> Peter C. Lai | University of Alabama-Birmingham
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Erik Marklund, PhD
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erikm at xray.bmc.uu.se
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