Dear Tsjerk and Ran,<br><br>I would like to try your modified versions of g_clustsize and trjconv as well<br>since I am facing similar issues on the analyses of micellar systems.<br><br>with kind regards,<br><br>Andre<br><br>
<div class="gmail_quote">On Thu, Apr 14, 2011 at 5:29 PM, jim jack <span dir="ltr"><<a href="mailto:blhawk13@yahoo.com">blhawk13@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
<div><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: 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><<a href="mailto:blhawk13@yahoo.com" target="_blank">blhawk13@yahoo.com</a>></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">
<br>From: jim jack <<a href="mailto:blhawk13@yahoo.com" target="_blank">blhawk13@yahoo.com</a>><br>Subject: micelles and trjconv -pbc cluster<br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Date: Thursday, April 14, 2011, 7:42 AM<div class="im"><br><br><div><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
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></div></blockquote></td></tr></tbody></table></div></td></tr></tbody></table><br>--<br>
gmx-users mailing list <a 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 <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 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></blockquote></div><br>