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<html><head><title>Re[2]: [gmx-users] how to get averaged coordinates for a residue in a time interval?</title>
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<p>Hi all,</p>
<p><br></p>
<p>One more similar question:</p>
<p><br></p>
<p>How can I get (in the quickest way!) any form of the Lindemann parameter for rather big molecular crystal? </p>
<p>(I mean averaged relative fluctuations in the intermolecular distance)</p>
<p><br></p>
<p><span class=rvts6>> Well, you could also use g_rmsf with -b and -e, and a suitable index file...</span></p>
<p><br></p>
<p><span class=rvts6>> Cheers,</span></p>
<p><br></p>
<p><span class=rvts6>> Tsjerk</span></p>
<p><br></p>
<p><span class=rvts6>> On Thu, Apr 1, 2010 at 6:18 PM, Justin A. Lemkul <</span><a class=rvts7 href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><span class=rvts8>> wrote:</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts9>>> Wu Rongqin wrote:</span></p>
<p><br></p>
<p><span class=rvts6>>>> Dear all,</span></p>
<p><br></p>
<p><span class=rvts6>>>> How to get the averaged coordinates for a short time range say, 10 ps?</span></p>
<p><span class=rvts6>>>> which utility should be used?</span></p>
<p><br></p>
<p><span class=rvts9>>> g_traj to extract the coordinates, g_analyze to do averaging.</span></p>
<p><br></p>
<p><span class=rvts9>>> -Justin</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts6>>>> r. q.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts9>>> --</span></p>
<p><span class=rvts9>>> ========================================</span></p>
<p><br></p>
<p><span class=rvts9>>> Justin A. Lemkul</span></p>
<p><span class=rvts9>>> Ph.D. Candidate</span></p>
<p><span class=rvts9>>> ICTAS Doctoral Scholar</span></p>
<p><span class=rvts9>>> MILES-IGERT Trainee</span></p>
<p><span class=rvts9>>> Department of Biochemistry</span></p>
<p><span class=rvts9>>> Virginia Tech</span></p>
<p><span class=rvts9>>> Blacksburg, VA</span></p>
<p><span class=rvts9>>> jalemkul[at]vt.edu | (540) 231-9080</span></p>
<p><a class=rvts7 href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></p>
<p><br></p>
<p><span class=rvts9>>> ========================================</span></p>
<p><span class=rvts9>>> --</span></p>
<p><span class=rvts9>>> gmx-users mailing list </span><a class=rvts7 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></p>
<p><a class=rvts7 href="http://lists.gromacs.org/mailman/listinfo/gmx-users">>> http://lists.gromacs.org/mailman/listinfo/gmx-users</a></p>
<p><span class=rvts9>>> Please search the archive at </span><a class=rvts7 href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class=rvts10> before posting!</span></p>
<p><span class=rvts9>>> Please don't post (un)subscribe requests to the list. Use the www interface</span></p>
<p><span class=rvts9>>> or send it to </span><a class=rvts7 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><span class=rvts10>.</span></p>
<p><span class=rvts9>>> Can't post? Read </span><a class=rvts7 href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts6>> -- </span></p>
<p><span class=rvts6>> Tsjerk A. Wassenaar, Ph.D.</span></p>
<p><br></p>
<p><span class=rvts6>> post-doctoral researcher</span></p>
<p><span class=rvts6>> Molecular Dynamics Group</span></p>
<p><span class=rvts6>> Groningen Institute for Biomolecular Research and Biotechnology</span></p>
<p><span class=rvts6>> University of Groningen</span></p>
<p><span class=rvts6>> The Netherlands</span></p>
<p><span class=rvts11><br></span></p>
<p><span class=rvts11>-- </span></p>
<p><span class=rvts11>Regards,</span></p>
<p><span class=rvts11> Dmitri </span><a class=rvts12 href="mailto:ddubov@ngs.ru">mailto:ddubov@ngs.ru</a></p>
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