<br /><br /><span>On 05/07/11, <b class="name">balaji nagarajan </b> <balaji_sethu@hotmail.com> wrote:</span><blockquote cite="mid:SNT123-W85C277A8A509D12A42F66E25F0@phx.gbl" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p>
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<br />Dear Users ! <br /><br />I have a doubt in minimizing the structure with water box ! </div></td></tr></tbody></table></p></span></div></blockquote><br />Go easy on the exclamation marks - who's going to attract a higher quality answer, someone who sounds like a mature professional, or an excited kid? :-)<br /><br /><blockquote cite="mid:SNT123-W85C277A8A509D12A42F66E25F0@phx.gbl" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><table><tbody><tr><td class="hmmessage"><div dir="ltr">I have taken a penta peptide and solvated it with spce water box ! <br /><br />I have minimized the system with the minim.mdp file which i have attached ! ( i have used steep option ) <br /><br />when I calculated the protein- protein and protein-solvent interaction energy <br /><br />the protein-protein energy have not fall down much ! </div></td></tr></tbody></table></p></span></div></blockquote><br />Maybe it was near a minimum already. Maybe the solvent is locking the protein in place. Maybe it doesn't matter.<br /><br /><blockquote cite="mid:SNT123-W85C277A8A509D12A42F66E25F0@phx.gbl" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><table><tbody><tr><td class="hmmessage"><div dir="ltr">and i tried with various options in the mdp options " emtol "<br /><br /><br />(how to know that the system is entirely minimized ! what is the criteria to be fixed on regarding a <br />small peptide )</div></td></tr></tbody></table></p></span></div></blockquote><br />That depends on the purpose. Do check out all the tutorial material you can put your hands on. Google is your friend.<br /><br /><blockquote cite="mid:SNT123-W85C277A8A509D12A42F66E25F0@phx.gbl" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><table><tbody><tr><td class="hmmessage"><div dir="ltr">when i have the option 6 of the file ( Coulomb-14 ) for the first step and the last step ! </div></td></tr></tbody></table></p></span></div></blockquote><br />What's your question?<br /><br />Mark<br /><blockquote cite="mid:SNT123-W85C277A8A509D12A42F66E25F0@phx.gbl" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span><p><table><tbody><tr><td class="hmmessage"><div dir="ltr"><br />Statistics over 1 steps [ 0.0000 through 0.0000 ps ], 1 data sets<br />All statistics are over 1 points<br /><br />Energy Average Err.Est. RMSD Tot-Drift<br />-------------------------------------------------------------------------------<br />Coulomb-14 908.433 -- 0 0 (kJ/mol)<br /><br /><br /><br /><br /><br /><br />Statistics over 1000 steps [ 0.0000 through 999.0000 ps ], 1 data sets<br />All statistics are over 2 points<br /><br />Energy Average Err.Est. RMSD Tot-Drift<br />-------------------------------------------------------------------------------<br />Coulomb-14 892.2 2.3 nan -16.4675 (kJ/mol)<br /><br /><br />------------------------------------------------------------------------<br />I have attached all the files below ! <br /><br />the script "test-script.sh " is to run all which i have done ! <br /><br />thanks in advance <br /><br /><br /> </div></td></tr></tbody></table>
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