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Thanks for the reply,<br>
<br>
Distance restraints won't to the job I suppose, since I'd need a second atom
to which<br>
the restraint refers to. I just do not want the atoms of the loop to move
too far from the<br>
current position, say only +/- 2 angstrom in all dimensions. Amber provides
such a<br>
feature but I don't know if it is possible to achieve this with Gromacs.
<br>
I have tried to define a set of atoms at exactly the same position as the
loop atoms,<br>
didn't define any bonds, pairs etc. for them, gave them zero charges and
applied position<br>
restraints. To these atoms I defined distance restraints for my real atoms,
however,<br>
the minimizations/simulations crashed. Is this procedure in general possible
and I<br>
did something wrong in the set up? If not, is there another, may be easier
way<br>
to do it?<br>
<br>
Thanks again,<br>
Uwe<br>
<br>
David van der Spoel wrote:<br>
<blockquote type="cite" cite="mid:1103117786.28446.36.camel@vangogh">
<pre wrap="">On Wed, 2004-12-15 at 12:53 +0100, Uwe Richter wrote:<br></pre>
<blockquote type="cite">
<pre wrap="">Dear all,<br><br>is there a way to let parts of a protein move only a certain<br>distance from the current position. I have a loop and I want<br>to relax it by high temperature MD or simulated annealing but<br>I don't want it to move too far away.<br></pre>
</blockquote>
<pre wrap=""><!---->Use distance restraints (not these are not constraints)<br></pre>
<blockquote type="cite">
<pre wrap="">Thanks for you help,<br>Uwe<br><br><br>_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></pre>
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