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<DIV><FONT face=Arial size=2>1) You can force "genbox" to insert extramolecules
of solvent in your box.</FONT></DIV>
<DIV><FONT face=Arial size=2> And equilibrate the whole thing,
but your peptide conformations have </FONT></DIV>
<DIV><FONT face=Arial size=2> been generated without solvent,
right ! HOw good is that ? I am not sure.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>2) You can re-do your SAs with explicit solvent !
You beggin with a conformation</FONT></DIV>
<DIV><FONT face=Arial size=2> of your peptide. You heat it up
to 1000 K run for 50 ps and begin to cool down.</FONT></DIV>
<DIV><FONT face=Arial size=2> Much longer, but the size
</FONT><FONT face=Arial size=2>of the system is small. You can compare the
</FONT></DIV>
<DIV><FONT face=Arial size=2> structures at the end of the
50ps at 1000K and see if they are different enough.</FONT></DIV>
<DIV><FONT face=Arial size=2> If they are you are can assume
that you are going to explore enough space.</FONT></DIV>
<DIV><FONT face=Arial size=2> ideally. But I'd do more
SAs.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Good luck</FONT></DIV>
<DIV><FONT face=Arial size=2>XAvier</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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