<HTML><BODY>Greetings!<br><br>I wounder to know about algoritms of energy minimization presented in the MMTK. What exactly type of that algoritms is most suitable for the common proteins ( 2000-5000 atoms ) ?  I've tried to use the example script<span class="c"> for energy minimization</span><br><pre><span class="n">minimizer</span> <span class="o">=</span> <span class="n">ConjugateGradientMinimizer</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span><br>                                       <span class="n">actions</span><span class="o">=</span><span class="p">[</span><span class="n">StandardLogOutput</span><span class="p">(</span><span class="mi">50</span><span class="p">)])</span><br><span class="n">minimizer</span><span class="p">(</span><span class="n">convergence</span> <span class="o">=</span> <span class="mf">1.e-3</span><span class="p">,</span> <span class="n">steps</span> <span class="o">=</span> <span class="mi">10000</span><span class="p">)<br><br></span><br>but this is very slow for my proteins ( I've tested different proteins like typical globular lyzocyme).<br><br>What average number of steps I should define for my proteins for obtaining well minimized universe  ? Also I wounder to know about minimization of membrane proteins? Does this<br>procedure must be conducted in the explicit membrane environment or the simulation in the vacuum would be reasonable?<br><br>Finally small qustion about scripting :) If I save my universe in pdb after minimization e.g<br><br></pre><pre><br><span class="n">universe</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">(</span><span class="n">Amber94ForceField</span><span class="p">())</span><br><span class="n">universe</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="s">'bala1'</span><span class="p">)</span><br><br><br><span class="n">minimizer</span> <span class="o">=</span> <span class="n">ConjugateGradientMinimizer</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span><br>                                       <span class="n">actions</span><span class="o">=</span><span class="p">[</span><span class="n">StandardLogOutput</span><span class="p">(</span><span class="mi">50</span><span class="p">)])</span><br><span class="n">minimizer</span><span class="p">(</span><span class="n">convergence</span> <span class="o">=</span> <span class="mf">1.e-3</span><span class="p">,</span> <span class="n">steps</span> <span class="o">=</span> <span class="mi">10000</span><span class="p">)</span><br><br></pre><pre><span class="n">universe</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="s">'insulin_with_h.pdb'</span><span class="p">)</span><br><br>does I obtain minimized structure of my protein?<br><br>Thank you for your help,<br><br>Gleb<br><br></pre><pre><br><br></pre><pre><br><br></pre><br></BODY></HTML>