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Dear Stanislav,<br>
<br>
AFAIK there's no "targeted MD" in GMX. You can run EDS or use the
flooding algorithm. <br>
<br>
Ran.<br>
<br>
Stanislav Bobritsky wrote:
<blockquote
cite="mid34c162b50801090441v7e8ec048ha4e427261dcb43ca@mail.gmail.com"
type="cite">Hello dear gromacs users!<br>
I`m trying to do targeted MD. I have two protein conformations which
are different from each other by one loop position. I need to force
conformation A to B.<br>
It was following commands executed:
<br>
<br>
grompp -Ó box.gro -f md.mdp -r conf1.pdb -rb conf2.pdb -p topol.top -o
transformer.tpr<br>
<br>
mdrun -s transformer.tpr -o -x -c -e -g -v <br>
<br>
But it can be viewed from traj.xtc that conformation didn`t change.
Protein just spins (with speed increasing), and desired loop does not
move.
<br>
<br>
What can I do to fix it?<br>
<br>
<span><span>Best regards, Stanislav Bobritsky,š <br>
<br>
ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.</span></span><br>
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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
------------------------------------------------------
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