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Hello,<br>
<br>
Dastmalchi wrote:<br>
<blockquote type="cite"
cite="mid003c01c4ebe4$d5d71510$1c7da8c0@res.tbzmed.ac.ir">
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<div><font face="Arial" size="2">Hi there,</font></div>
<div> </div>
<div><font face="Arial" size="2">1) I want to keep the secondary
structure conformations in different parts of my protein structure
fixed, say for example, residues 20-40, 60-80, and 90-100 needs to be
remained in helical conformation during the MD simulation. I would have
thought that constraining the hydrogen bonds will do the job, so I was
experimenting on a small helical peptide and put "Constraints = hbonds"
in the md.mdp file. However, during a short MD the peptide did not keep
its helical conformation and the number of h-bonds was changing during
the MD.</font></div>
<div><font face="Arial" size="2">## Is this the right way for fixing
the secondary structure?</font></div>
</blockquote>
No. Constraints = hbonds will constrain the length of bonds containing
hydrogen atoms.<br>
<blockquote type="cite"
cite="mid003c01c4ebe4$d5d71510$1c7da8c0@res.tbzmed.ac.ir">
<div><font face="Arial" size="2">## Maybe I need to set some kind of
force constant for this to happen. Is that right?</font></div>
<div><font face="Arial" size="2">## As I mentioned above I want this
in different parts of protein. Do I need to assign these parts
different groups and somehow tell the Constraints = hbonds to just
apply the constraints on these groups?</font></div>
<div><font face="Arial" size="2">## How can I assign different parts
as different groups?</font></div>
<div> </div>
<div><font face="Arial" size="2">2) How can I apply the "Define =
-DPOSERS" to different parts in the structure?</font></div>
</blockquote>
I think that the simplest solution to your problem will be to edit the
posre file.
<blockquote type="cite"
cite="mid003c01c4ebe4$d5d71510$1c7da8c0@res.tbzmed.ac.ir">
<div> </div>
<div><font face="Arial" size="2">Thanks for your kind help.</font></div>
<div> </div>
<div><font face="Arial" size="2">Cheers, Siavoush</font></div>
<div> </div>
<div> </div>
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<br>
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</blockquote>
Ran.<br>
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