<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hello Tsjerk,</span></div><div><br><span></span></div><div><span>Thank you very much, you're right, but I saw in several articles that had used from this for confirmation of results of gyration, or to obtain the radius of hydrocarbon core (by rms distance from the carbon bounded with head group to the micelle COM).</span></div><div><span>I also used from g_rmsdist, but it dose not have anything to determine center of mass of micelle. <br></span></div><div><br><span></span></div><div><span>Best Regards</span></div><div>Dina<br><span></span></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;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span
style="font-weight:bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> dina dusti <dinadusti@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, January 29, 2012 11:26 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] root-mean-square distance<br> </font> </div> <br>
Hi Dina,<br><br>The radius of gyration is defined as sqrt( (1/N) tr X'(I-jj')X ),<br>which is the RMSD w.r.t. to the center of mass. It's the same thing.<br>But I was talking about the tools g_gyrate and g_rms. The latter fits<br>the structure to the reference structure and then sums the distances<br>between paired atoms. That only works if you have a reference with all<br>coordinates set to (0,0,0). But then the answer will be identical to<br>that of g_gyrate, so why bother? Use g_gyrate, because it does what<br>you want.<br><br>Cheers,<br><br>Tsjerk<br><br>On Sun, Jan 29, 2012 at 8:07 PM, dina dusti <<a ymailto="mailto:dinadusti@yahoo.com" href="mailto:dinadusti@yahoo.com">dinadusti@yahoo.com</a>> wrote:<br>> Hello Tsjerk,<br>><br>> Thank you from your reply, but in the many papers, radius of micelle has<br>> been obtained from both of them (i.e. gyration and root-mean-square distance<br>> from center of mass of micelle). I don't
know that how should I compute the<br>> radius of a spherical micelle from rms distance of the headgroup atoms from<br>> the micelle center of mass.<br>> May I ask you to help me?<br>><br>> Best Regards<br>> Dina<br>><br>> ________________________________<br>> From: Tsjerk Wassenaar <<a ymailto="mailto:tsjerkw@gmail.com" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>> To: dina dusti <<a ymailto="mailto:dinadusti@yahoo.com" href="mailto:dinadusti@yahoo.com">dinadusti@yahoo.com</a>>; Discussion list for GROMACS users<br>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Sunday, January 29, 2012 2:02 PM<br>> Subject: Re: [gmx-users] root-mean-square distance<br>><br>> Hi Dina,<br>><br>> g_rms calculates the RMS from pairwise distances after performing a<br>> least-squares fit. That's quite different from
what you want, and<br>> actually is what you get from g_gyrate...<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>> On Sun, Jan 29, 2012 at 8:09 AM, dina dusti <<a ymailto="mailto:dinadusti@yahoo.com" href="mailto:dinadusti@yahoo.com">dinadusti@yahoo.com</a>> wrote:<br>>> Dear Specialists,<br>>><br>>> I have a problem about computing of radius of micelle by<br>>> root-mean-square-distance. Please help me.<br>>> I obtained radius of my micelle 2.4 nm by g_gyrate.<br>>> g_gyrate -f md.xtc -s md.tpr -o gyrate.xvg -b 150000<br>>> I want compare it by rms distance.<br>>> I use from g_rms as following:<br>>> g_rms -f md.xtc -s md.tpr -o distrmsd.xvg -n index.ndx -b 150000<br>>> It result me 3.992290e+00 nm after averaging by g_analyze -f distrmsd.xvg<br>>> -av<br>>> (the radius of a spherical micelle is defined as the rms distance of the<br>>> headgroup atoms
from the micelle center of mass, how should I define com<br>>> of<br>>> micelle in g_rms?)<br>>> I think I am wrong somewhere.<br>>> May I ask you to help me,Please?<br>>><br>>> Best Regards<br>>> Dina<br>>><br>>> --<br>>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>>> Please search the archive at<br>>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>> Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists<br>><br>><br>><br>> --<br>> Tsjerk A. Wassenaar, Ph.D.<br>><br>> post-doctoral researcher<br>> Molecular Dynamics Group<br>> * Groningen Institute for Biomolecular Research and Biotechnology<br>> * Zernike Institute for Advanced Materials<br>> University of Groningen<br>> The Netherlands<br>><br>><br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>>
www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br><br><br> </div> </div> </div></body></html>