<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 from your reply, but in the many papers, radius of micelle has been obtained from both of them (i.e. gyration and root-mean-square distance from center of mass of micelle). I don't know that how should I compute </span>the radius of a spherical micelle from rms distance of the headgroup atoms from the micelle center of mass. <br></div><div>May I ask you to help me?</div><div><br></div><div>Best Regards</div><div>Dina<br></div><div><br></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 2:02 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>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 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> </div> </div> </div></body></html>