[gmx-users] Trajectories

[Erik Marklund]

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,
>> Blake
>> 
>> --
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> -- 
> ==================================================================
> Peter C. Lai			| University of Alabama-Birmingham
> Programmer/Analyst		| KAUL 752A
> Genetics, Div. of Research	| 705 South 20th Street
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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