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<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>Dear
all,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=390024712-02012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>Now I have 3
questions.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=390024712-02012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>1) Do I need to use
genbox to add H2O twice?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>In the past, I first
used genbox to add H2O and then used genion to add counterion. After that is EM.
But now I find, if I use genbox again after genion or even after EM, there are
some additional, though very few, H2O molecules will be added into system. So I
want to ask if the method to use genbox twice is more
reasonable?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=390024712-02012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>2)One or two
EM?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>Some users mention
that one EM will be done after adding H2O and the second will be done after
adding counterion. In the past, I just did one EM only after adding counterion.
Is it more reasonable to do one EM right after adding H2O?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=390024712-02012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>3) bond-length
constraint in EM or not?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>In the past, I did
EM without bond-length constraint. But lately one person, who is
obviously more expericed in MD than me, told me that I should do 2 EM, 1st
with bond-length constraint and 2nd without it. Is it more
reasonable?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=390024712-02012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=390024712-02012007>Any comments are
welcome.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV align=left>
<DIV align=left><FONT face="Times New Roman" size=4>Zhongqiao Hu</FONT></DIV>
<DIV align=left><FONT face="Times New Roman"></FONT> </DIV>
<DIV align=left><FONT face="Times New Roman">Lab E5-04-27</FONT></DIV>
<DIV align=left>
<DIV align=left><FONT face="Times New Roman">Tel: 65161946(O)</FONT></DIV></DIV>
<DIV align=left><FONT face="Times New Roman">Department of Chemical and
Biomolecular Engineering</FONT></DIV>
<DIV align=left><FONT face="Times New Roman">National University of
Singapore</FONT></DIV>
<DIV align=left><FONT face="Times New Roman">117576, Singapore</FONT></DIV>
<DIV align=left><FONT face="Times New Roman"></FONT> </DIV></DIV>
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