<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div id="yiv343392827"><table cellspacing="0" cellpadding="0" border="0" id="yiv343392827bodyDrftID" class="yiv343392827"><tbody><tr><td id="yiv343392827drftMsgContent" style="font:inherit;font-family:arial;font-size:10pt;"><p>Dear Ran Friedman and Tsjerk Wassennaar,</p><p><br></p><p> First of all, thanks to all responses to my problem. As far as the modified versions of g_clustsize and trjconv, I really want to try them. </p><p> </p><p>Best regards <br></p><p><br></p><p>George Koros</p><br>--- On <b>Thu, 4/14/11, jim jack <i><blhawk13@yahoo.com></i></b> wrote:<br><blockquote style="border-left:2px solid rgb(16, 16, 255);margin-left:5px;padding-left:5px;"><br>From: jim jack <blhawk13@yahoo.com><br>Subject: micelles and trjconv -pbc cluster<br>To: gmx-users@gromacs.org<br>Date: Thursday, April 14, 2011, 7:42 AM<br><br><div
id="yiv343392827"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font:inherit;">Dear GROMACS users,
<br><br> I am trying to simulate an SDS micelle in water. As simulation time goes by, the micelle approaches the edge of the box and consequently some of these molecules get in from the other side. This leads to incorrect radius of gyration, eccentricity, etc. A solution to this problem is the option <span style="font-style:italic;">trjconv -pbc cluste</span>r as described in the page <a rel="nofollow">http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering</a>. In this case, the problem is that it takes a lot of time and a huge file (several GB) is created due to this procedure. Is there any other alternative?<br><br>Thanks in advance<br><br>George Koros<br><br></td></tr></tbody></table></div></blockquote></td></tr></tbody></table></div></td></tr></table>