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<p class=MsoNormal>Hello all Gromacs users,<o:p></o:p></p>
<p class=MsoNormal>I’m simulating a 255 a.a peptide which is only a
segment of a whole protein.<o:p></o:p></p>
<p class=MsoNormal>I’m using the triclinic box with -d 1.2 nm.<o:p></o:p></p>
<p class=MsoNormal>Because the peptide is only a segment out of a larger
protein I would like to restrain the ends of the peptide in order to prevent
the peptide <o:p></o:p></p>
<p class=MsoNormal>from closing on its self during the simulation.<o:p></o:p></p>
<p class=MsoNormal>I thought to apply distance restraint in order to do so.<o:p></o:p></p>
<p class=MsoNormal>Using VMD I measured the distance between the C-alphas of
the first and last a.a. of the peptide and got 88.8A.<o:p></o:p></p>
<p class=MsoNormal>I wanted to double check the distance, so I used g_dist and
g_mindist and got a 56A!!! <o:p></o:p></p>
<p class=MsoNormal>I guess that PBC is the reason for the difference.<o:p></o:p></p>
<p class=MsoNormal>Which distance (VMD or Gromacs) should I use when applying
the distance restraint? <o:p></o:p></p>
<p class=MsoNormal>Is such a distance restrain (88.8A) even possible? (too
long?)<o:p></o:p></p>
<p class=MsoNormal>I would be glad to learn any other way to enforce a minimal
movement of the ends of the peptide.<o:p></o:p></p>
<p class=MsoNormal>Thanks in advance,<o:p></o:p></p>
<p class=MsoNormal>Udi<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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