<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 7:01 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; ">I wish I could use a picture :)<br>Unfortunately, this is not possible since I need the energy value to be able to compare this to other mutations of the same structure and to provide a "measure" of how energetically favourable one is in comparison to the other.</div></span></blockquote>Ok, that is what I was suspecting ... then you should be really careful in using the minimized </div><div>energy as a "measure" of the different effect of the mutations in protein. This has probably </div><div>not much value! </div><div>You'd need to go to the free energy and not the enthalpy (potential energy) of one minimized frame<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; "><br>And I am using a box of water because I feel that provides a better estimation of natural conditions than a vaccum :)<br></div></span></blockquote>In that case I am afraid the water should be relaxed ... equilibrated if you prefer.</div><div>Its interaction with the protein is probably no-sense. A minimization is not</div><div>sufficient to fix it.</div><div><br></div><div><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; "><font class="Apple-style-span" face="Helvetica"><span class="Apple-style-span" style="font-size: medium;"><br></span></font></div></span></blockquote><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; "><span class="Apple-converted-space"> </span><br><br><hr>Hotmail: Powerful Free email with security by Microsoft.<span class="Apple-converted-space"> </span><a href="https://signup.live.com/signup.aspx?id=60969" target="_new">Get it 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. 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