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<DIV><FONT face=Arial size=2><SPAN class=564284901-15092006>Dear
all,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=564284901-15092006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=564284901-15092006>I finish a 10-ns MD
simulations for a system including 16 lysozyme molecule chains, some solvents
H2O molecules and 128 Cl- counter ions under PBC. When I use the command to
calculate the RMSF of residues as follows:</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=564284901-15092006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=564284901-15092006>g_rmsf -f ***.xtc -s
***.tpr -o rmsf_res.xvg (I selected 3 for groups)</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=564284901-15092006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=564284901-15092006>The results showed
that 3rd and 14the chain had RMSF 1.2-2nm, which is obviously unreasonable. But
compared with other chains, these 2 chains have the basically same peak places.
The difference is that RMSFs of residues in these 2 chains are systematically
much higher. Is there a bug resulting in a systematic error
or any other reasons? Any suggestions are welcome.
Thanks,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=564284901-15092006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=564284901-15092006>Zhongqiao
Hu</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=564284901-15092006>Dept of Chemical and
Biomolecular Engineering</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=564284901-15092006>National University
of Singapore </SPAN></FONT></DIV></BODY></HTML>