<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>The distortion of a protein starting structure can result from various reasons:<div>1- experimental determination of the structure: this include the experimental</div><div>conditions (T, pH) as well as the crystal contacts if X-ray were used, dynamics</div><div>of some part of the molecule if NMR.</div><div>2- the manner you solvate and equilibrate. Using position restrain on the </div><div>heavy atoms of the protein first, and then on the Calphas is generally a good</div><div>idea. The time you need to run those simulations depends on the system. If</div><div>you see deviations you can try to run a bit longer. 100 ps is generally sufficient</div><div>but can be extended to 500 ps, this is no problem.</div><div>3- the force field you are using might also trigger some "small" deviations of the </div><div>protein. The protein structure might contain "strange" local configuration that</div><div>are not sable in the FF. </div><div>4- you set up, meaning time step, temperature, pressure, ...</div><div><br></div><div>Note finally that a deviation from the starting structure might just be a fluctuation</div><div>of a labile region of the protein ... </div><div><br></div><div><div><div>On Apr 15, 2010, at 8:40 AM, sonali dhindwal wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font: inherit;">Hello All,<br>I have a protein of 576 amino acid long, and has a barell shape topolgy.<br>I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small.<br>I wrote this query before also, can it be possible that this is due to equilibration conditons i am giving, i am equilibrating it for 100 ps under NVT using brendenson coupling.<br>What should be ideal time for equibrating the protein with solvent ?<br>How should it be determined, or it is based on experimenting with different conditions ?<br>Please help.<br>Regards.<br><div>--<br>Sonali Dhindwal</div></td></tr></tbody></table><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></body></html>