<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=us-ascii">
<META content="MSHTML 6.00.2900.2963" name=GENERATOR></HEAD>
<BODY>
<DIV><FONT face=Arial><FONT size=2><SPAN class=052053809-15092006>>
</SPAN>are all the lysozymes treated as one protein? in that case it might be a
PBC artifact. try doing the rmsf per molecule (by running the program
16<BR><SPAN class=052053809-15092006>> </SPAN>times) and then overlaying the
result.</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial><FONT size=2><SPAN class=052053809-15092006>>
</SPAN>are you trying to crystallize it?</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><BR><SPAN
class=052053809-15092006>></SPAN>David.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><SPAN class=052053809-15092006><FONT face=Arial size=2>Thank David. I just
found that it was due to jumps in trajectory files. I saw the animation of
trajetory file and found some protein molecules jumped from one side to the
other side. Thus I produced a new trajectory files using trjconv with
option "-pbc nojump" and then calculated RMSF, the result seems OK. So
it is a little strange that g_rmsf can not recognize some information about
jumps in trajectory file. If it is, could you repair it in the next
release?</FONT></SPAN></DIV>
<DIV><SPAN class=052053809-15092006><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=052053809-15092006><FONT face=Arial
size=2>Thanks,</FONT></SPAN></DIV>
<DIV><SPAN class=052053809-15092006><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=052053809-15092006><FONT face=Arial size=2>Zhongqiao
Hu</FONT></SPAN></DIV>
<DIV><SPAN class=052053809-15092006><FONT face=Arial size=2>Dept of Chemical and
Biomolecular Engi.</FONT></SPAN></DIV>
<DIV><SPAN class=052053809-15092006><FONT face=Arial size=2>National Univ. of
Singapore</FONT></SPAN></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2><BR></FONT> </DIV></BODY></HTML>