<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=gb2312">
<META content="MSHTML 6.00.6000.17092" name=GENERATOR><LINK 
href="BLOCKQUOTE{margin-Top: 0px; margin-Bottom: 0px; margin-Left: 2em}" 
rel=stylesheet></HEAD>
<BODY style="FONT-SIZE: 10pt; MARGIN: 10px; FONT-FAMILY: verdana">
<DIV><FONT face=Verdana size=2>
<DIV>Hi,&nbsp;gmx-users</DIV>
<DIV>&nbsp;</DIV>
<DIV></DIV>
<DIV>&nbsp;&nbsp;&nbsp;&nbsp;I&nbsp;want&nbsp;to&nbsp;know&nbsp;whether&nbsp;the&nbsp;g_cluster&nbsp;is&nbsp;appropriate&nbsp;to&nbsp;analyze&nbsp;clusters&nbsp;of&nbsp;conformations&nbsp;of&nbsp;a&nbsp;structure&nbsp;from&nbsp;a&nbsp;trajectory,&nbsp;and&nbsp;how&nbsp;to&nbsp;use&nbsp;it&nbsp;correctly&nbsp;to&nbsp;attain&nbsp;the&nbsp;right&nbsp;results?&nbsp;</DIV>
<DIV>&nbsp;&nbsp; 
&nbsp;I&nbsp;try&nbsp;to&nbsp;analyze&nbsp;the&nbsp;clusters&nbsp;of&nbsp;conformations&nbsp;of&nbsp;a&nbsp;structure&nbsp;using&nbsp;g_cluster.&nbsp;But&nbsp;the&nbsp;output&nbsp;*.pdb&nbsp;clusters&nbsp;file&nbsp;seemed&nbsp;not&nbsp;to&nbsp;be&nbsp;right.</DIV>
<DIV></DIV>
<DIV>&nbsp;&nbsp;&nbsp; 
g_cluster&nbsp;-f&nbsp;*.xtc&nbsp;-s&nbsp;*.tpr&nbsp;-wcl&nbsp;10&nbsp;-cutoff&nbsp;0.1&nbsp;-method&nbsp;-linkage;&nbsp;the&nbsp;only&nbsp;1&nbsp;cluster&nbsp;was&nbsp;found.&nbsp;And&nbsp;the&nbsp;results&nbsp;are&nbsp;different&nbsp;when&nbsp;I&nbsp;add&nbsp;the&nbsp;option&nbsp;-&nbsp;&nbsp;&nbsp; 
fit&nbsp;or&nbsp;-nofit.&nbsp;&nbsp;The&nbsp;explanation&nbsp;of&nbsp;manual&nbsp;to&nbsp;the&nbsp;option&nbsp;-fit&nbsp;is&nbsp;using&nbsp;least&nbsp;squares&nbsp;fitting&nbsp;before&nbsp;RMSD&nbsp;calculation.&nbsp;what&nbsp;is&nbsp;the&nbsp;meaning&nbsp;about&nbsp;it&nbsp;in&nbsp;detail?</DIV>
<DIV></DIV>
<DIV>Thanks&nbsp;for&nbsp;great&nbsp;help.</DIV>
<DIV>&nbsp;</DIV>
<DIV></DIV>
<DIV>Yours&nbsp;Sincerely</DIV>
<DIV>&nbsp;</DIV>
<DIV></DIV>
<DIV>Duan&nbsp;baogen</DIV></FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT>&nbsp;</DIV></BODY></HTML>