<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear Prof.</div><div><br></div><div>Thank you very much from your help.</div><div><br></div><div>Best Regards</div><div>Dina</div><div>--------------------------------------------------------------------------------------------------------------------------------------------------------------</div><div>On 3/02/2012 3:17 AM, dina dusti wrote:<br>> Dear Prof<br>><br>> Thank you very much from your response.<br>> She said me:<br>> "In g_dist, when you select two groups for distance calculation, it <br>> computes the distance between COM's of groups. Now, what is expected <br>> for the distance between the micelle's COM and the COM of (e.g.) head <br>> groups? Clearly, it's near zero ! So you should first calculate the <br>> distance for each group separately and then average over all
distances."<br>><br>> But I didn't understand what was her mean about "you should first <br>> calculate the distance for each group separately and then average over <br>> all distances.", because I did g_dist between micelle and for example <br>> head group and then used g_analyze for dist.xvg and I had the quantity <br>> near zero!!!<br>><br><br>This can be done more efficiently with g_bond, treating each <br>head-to-tail distance as a "bond".<br><br>Mark</div></div></body></html>