<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear Prof.<br></span></div><div><span><br></span></div><div><span>Thank you very much from your response.</span></div><div><span> but I didn't select </span>micelle headgroups and then terminal carbon atom but also I selected COM of micelle and for example head group of micelle! The calulation of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but g_dist ...!!!</div><div>Where is my mistake?</div><div>I select groups in index file correctly.</div><div>Please help me.</div><div><br></div><div>Thank you again.</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> Justin A. Lemkul <jalemkul@vt.edu><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> Wednesday, February 1, 2012 3:13 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] g_dist<br> </font> </div> <br>
<br><br>dina dusti wrote:<br>> Dear Prof.<br>> <br>> Thank you very much from your response.<br>> Yes, dist.xvg has four column consists origin distance and distances in direction x, y , z. So distance that I want according to result of g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and the last carbon bounded with head group for index file.<br>> Also, I did this job for micelle and head group, and micelle with other groups but my results (distances) were all of them near the zero.<br>> Please help me to obtain correct distance.<br>> <br><br>Keep in mind what g_dist is measuring, center-of-mass distances. If you select the micelle headgroups and then terminal carbon atoms, the positions will be almost coincident, as your result suggests. Other groups that are giving a nearly-zero distance are likely coincident in the same manner.<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]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br> </div> </div> </div></body></html>