<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><br></span></div><div>Hi Justin,</div><div><br></div><div>Thanks for your hints. I feel the string in g_select is pretty much like tck/tl in VMD. <br></div><div>However I have not figured out the way to select a customized group defined in .ndx file.</div><div><br></div><div>And one more question I have, maybe more general, if I have, say, 100 frames, g_select will give me 100 dynamic indices in the .ndx file,</div><div>I am wondering if there is a way (might be some script) that can help me choose automatically for further processing, like g_hbond, and then I can program to collect all frames and average them.</div><div>In other words, there many commands in gromacs that require users to "Select a group", I am wondering if I can make this "choice" in a script rather than when I see the
prompt.</div><div><br></div><div>thanks,</div><div><br></div><div>Yao<br></div><div><br></div><div></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Yao Yao <yao0o@ymail.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, November 30, 2011 1:57 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] g_select dynamic indices<br> </font> <br>
<br><br>Yao Yao wrote:<br>> Hi Gmxers,<br>> <br>> I used g_dist to find all water molecules within 5 Angstrom of a protein in a trajectory with a little surprise that gromacs directly prints out those water on my screen rather than in an output file.<br><br>According to g_dist -h, that's what you should expect :)<br><br>> Since in each frame, those water molecules are not the same, I realize I need to make a dynamic index or indices for them.<br>> However I do not see any flag I could possibly introduce those water in g_select and then use -on flag to produce a dynamic index.<br><br>The index groups are output by g_select. Try g_select -select "help all" for examples of how to create groups.<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu |
(540) 231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br> </div> </div> </div></body></html>