<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<TITLE>Message</TITLE>
<META content="MSHTML 6.00.2900.2523" name=GENERATOR></HEAD>
<BODY>
<DIV><SPAN class=854500416-14102005><FONT face=Arial color=#0000ff size=2>I'm
trying to simulate an RNA molecule and it seems to simulate normal with the sd
integrator, but if I just change that one parameter to md the results
are incorrect. The molecule quickly (<100,000 steps) collapses
into a nested ball. Any ideas what is happening here?</FONT></SPAN></DIV>
<DIV><SPAN class=854500416-14102005><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=854500416-14102005><FONT face=Arial color=#0000ff
size=2>Thanks,</FONT></SPAN></DIV>
<DIV><SPAN class=854500416-14102005><FONT face=Arial color=#0000ff
size=2>--Scott</FONT></SPAN></DIV>
<DIV><FONT size=+0><FONT face=Arial><FONT color=#0000ff
size=2></FONT> </DIV></FONT><!--endarticle--></FONT></BODY></HTML>