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<DIV><FONT face=Arial size=2>Hi there,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>1) I want to keep the secondary structure
conformations in different parts of my protein structure fixed, say for
example, residues 20-40, 60-80, and 90-100 needs to be remained in helical
conformation during the MD simulation. I would have thought that constraining
the hydrogen bonds will do the job, so I was experimenting on a small
helical peptide and put "Constraints = hbonds" in the md.mdp file. However,
during a short MD the peptide did not keep its helical conformation and the
number of h-bonds was changing during the MD.</FONT></DIV>
<DIV><FONT face=Arial size=2>## Is this the right way for fixing the secondary
structure?</FONT></DIV>
<DIV><FONT face=Arial size=2>## Maybe I need to set some kind of force constant
for this to happen. Is that right?</FONT></DIV>
<DIV><FONT face=Arial size=2>## As I mentioned above I want this in different
parts of protein. Do I need to assign these parts different groups and somehow
tell the Constraints = hbonds to just apply the constraints on these
groups?</FONT></DIV>
<DIV><FONT face=Arial size=2>## How can I assign different parts as different
groups?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>2) How can I apply the "Define = -DPOSERS" to
different parts in the structure?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks for your kind help.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Cheers, Siavoush</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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