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 >> >> -- >> 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. >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > [email protected] | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- 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 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
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