Hi,<BR>I am new to GROMACS. I want to perform Normal Mode Analysis of a protein. For that I require a well minimized structure. I have minimized my structure using steepest descent and conjugate gradient. But the structure seems to have got struct in a local energy minima. How should I proceed to get a well minimized structure in order to go for Normal mode Analysis? <BR>Please suggest any protocol.<BR><BR>Regards,<BR clear=all><BR><BR><DIV><FONT color=#0000bf size=4></FONT> </DIV> <DIV><FONT color=#0000bf><STRONG>Anirban Ghosh</STRONG></FONT></DIV> <DIV><FONT color=#0000bf><STRONG>M.Tech Bioinformatics</STRONG></FONT></DIV> <DIV><FONT color=#0000bf><STRONG>University of Hyderabad</STRONG></FONT></DIV> <DIV><FONT color=#0000bf><STRONG>Hyderabad - 500 046</STRONG></FONT></DIV> <DIV><FONT color=#0000bf><STRONG>Andhra Pradesh</STRONG></FONT></DIV> <DIV><FONT color=#0000bf><STRONG>India</STRONG></FONT></DIV><p> 
<hr size=1></hr>
Here’s a new way to find what you're looking for - <a href="http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/">Yahoo! Answers</a>