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On 31/01/2012 11:53 AM, Li SUN wrote:
<blockquote
cite="mid:CAOmm63L23UL7JGBwyzrehG1v6_NFmsgqXUvDM+KkX6ChmekTUA@mail.gmail.com"
type="cite">Hello,<br>
<br>
I am doing pulling simulations with GROMACS and would like to keep
the chirality of the protein along the trajectory otherwise the
protein will take the wrong chirality especially at long
extensions. I have checked that using the improper dihedral or
dihedral restraint can restrain the dihedral, but dihedral
restraint is not equivalent to chirality restraint.</blockquote>
<br>
Why not? See 4.2.11 of manual and figure 4.8.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAOmm63L23UL7JGBwyzrehG1v6_NFmsgqXUvDM+KkX6ChmekTUA@mail.gmail.com"
type="cite"> So I am wondering if there is a "chirality restraint"
somewhere in GROMACS. Otherwise I might have to modify the code...<br>
<br>
Thanks in advance!<br>
<br clear="all">
<br>
-- <br>
Li Sun<br>
Department of Physics<br>
University of California, San Diego<br>
<br>
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