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1) How can i use genbox to insert extramolecules of solvent?<br>
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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>
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<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>
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<div><font face="Arial" size="2">Good luck</font></div>
<div><font face="Arial" size="2">XAvier</font></div>
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