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On 18/03/2012 1:01 PM, NG HUI WEN wrote:
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<p>Hi all,</p>
<p> </p>
<p>I have a seemingly simple task that turned quite tricky here.
</p>
<p> </p>
<p>I am trying to perform energy minimization on a crystal
structure after adding hydrogen to the protein using pdb2gmx
(OPLS).</p>
<p> </p>
<p>The problem I am facing now is that after energy
minimization, the protein and water (originally in the protein
cavity) were found in completely different coordinate space.
Using "pbc box" in VMD, I found that the water was
found roughly at the original space but not the protein. </p>
<p> </p>
<p>I have tried (all turned out futile) </p>
<p>1) EM with and without pbc</p>
<p>2) position restraint the protein backbone and water</p>
<p> </p>
<p>Would someone be able to help me on this? I know I must have
done something silly here.</p>
<p> <br>
</p>
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<br>
This is normal. See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>
<br>
Mark<br>
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