<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On May 3, 2010, at 6:40 PM, abdullah ahmed wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Actually I'd just like to know why both structures have such similar coloumb energy values.<span class="Apple-converted-space"> </span><br>If an electro-static interaction is being made in one structure and not in the other then their coloumb energy values should be different too, no? Wouldn't this be visible with simple energy minimisation? <span class="Apple-converted-space"> </span><br></div></span></blockquote>How different are they? </div><div><br></div><div>You mention you use encad with "full solvent". Does that mean you ahve the protein </div><div>solvated in a box of water? </div><div><br></div><div>If your point is only to show that in one case you have an electrostatic interaction and not</div><div>in the other you might just need to show that with an image! The energies after minimization </div><div>are not necessarily more meaningful ... </div><div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">I would prefer to not do molecular dynamics, because the structure is biologically optimal in this conformation and molecular dynamics may move it too much. <span class="Apple-converted-space"> </span><br><br><hr>Hotmail: Trusted email with Microsoft’s powerful SPAM protection.<span class="Apple-converted-space"> </span><a href="https://signup.live.com/signup.aspx?id=60969" target="_new">Sign up now.</a><span class="Apple-converted-space"> </span>--<span class="Apple-converted-space"> </span><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<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></body></html>