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<DIV><FONT face=Arial size=2><SPAN class=922285213-02012007>Thanks,
Tsjerk</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=922285213-02012007></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2>> >1) Do I need to use genbox to add H2O
twice?<BR>>> In the past, I first used genbox to add H2O and then used
genion to add<BR>>> counterion. After that is EM. But now I find, if I use
genbox again after<BR>>> genion or even after EM, there are some
additional, though very few, H2O<BR>>> molecules will be added into
system. So I want to ask if the method to use<BR>>> genbox twice is more
reasonable?<BR>>></FONT></DIV>
<DIV><FONT face=Arial size=2><BR>>Assuming that you mean placement inside a
protein, I don't think it is<BR>>necessary. For the solvent itself or the
interface, it really doesn't<BR>>matter. During EM, or even during MD, some
cavities may be generated<BR>>which could be filled with a water molecule,
but that doesn't mean<BR>>they should be occupied. Of course, it would be
interesting to test<BR>>whether your results improve, i.e. one or the other
leads to a more<BR>>stable system. In that case, you should also try the
placement of<BR>>water by optimization of the orientation (which isn't done
using<BR>>genbox and is much more costly).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><SPAN class=922285213-02012007><FONT face=Arial size=2>I am running MD
simulation in some protein crystals. I always find that the water density
in some big pore within protein crystals is ca. 950 or even 920 kg/m^3 at
300K and SPC model, obvioulsy less than 1000 kg/m^3 (bulk density). I think it
will be more reasonable if water density is closer to bulk density,
right?</FONT></SPAN></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>>> 2)One or two EM?<BR>>> Some users
mention that one EM will be done after adding H2O and the second<BR>>>
will be done after adding counterion. In the past, I just did one EM
only<BR>> >after adding counterion. Is it more reasonable to do one EM
right after<BR>>> adding H2O?<BR>>It's not likely to be necessary. EM
(prior to MD) is just to obtain a<BR>>reasonable structure which can be used
to start an MD run with,<BR>>without exploding due to bad contacts/strained
geometries.</FONT></DIV>
<DIV><SPAN class=922285213-02012007><FONT face=Arial size=2>You are right in
this point. I totally agree with you.</FONT></SPAN></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>>><BR>> >3) bond-length constraint in
EM or not?<BR>>> In the past, I did EM without bond-length constraint. But
lately one person,<BR>>> who is obviously more expericed in MD than me,
told me that I should do 2<BR>> >EM, 1st with bond-length constraint and
2nd without it. Is it more<BR>>> reasonable?<BR>>Again, not necessary,
see point 2.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><SPAN class=922285213-02012007><FONT face=Arial size=2>I wonder if the
structure of the system under the study is changed during EM. For example, in my
system consisting protein molecules, water and counterion, some bond lengths in
protein molecules will be changed if I do EM without bond-lenght
constraint. In this case, some changed bond lengths in EM will be kept
constant in equilibration and production MDs because I use bond-length
constraint. I doubt its validaty. So I am thinking if it is more reasonable to
carry out EM with bond-length constraint.</FONT></SPAN></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>><BR>>>Any comments are
welcome.</FONT></DIV>
<DIV><FONT face=Arial size=2><BR>>I hope this helps.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Cheers,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Tsjerk<BR></FONT></DIV>
<DIV> </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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