<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">All,<div><br></div><div>I just wanted to pass along the below e-mail, previously sent to the mailing list, and highlight the potential implications.</div><div><br></div><div>If I understand properly, there was a bug in all Gromacs versions beginning prior to 3.3 (probably not 3.1.4) and through 4.0.3 that affected the TIP4P and TIP4P-Ew water models, *unless* you were using separate energy groups for water and the rest of your system. Berk notes below that the bug "would cause a few tip4p-tip4p charge interactions to be missing". I want to emphasize that this is potentially an extremely serious problem.</div><div><br></div><div>In my own testing I found that with this bug, densities for TIP4P-Ew still came out close to the literature values, but it could result in substantial errors in other properties. For example, in computing hydration free energies with acetamide, I found my hydration free energies changed by more than 2 kcal/mol when I changed rcoulomb by 0.1 nm, even when using PME and long-ish real-space cutoffs, which should not be the case. </div><div><br></div><div>Secondarily, I found that my computed hydration free energies with either set of cutoffs disagreed with the "correct" values (as obtained by other simulation packages) by 0.7 to 3 kcal/mol depending on my choice of real-space cutoff. In contrast, with other water models, I could reproduce the expected values to within my computed uncertainties (+/-0.05 to 0.1 kcal/mol).</div><div><br></div><div>I am still doing some testing, but I anticipate that I will ultimately have to submit errata for two different papers I've published in which I used the TIP4P-Ew water model in combination with GROMACS. I urge you to check your own studies that have used TIP4P/TIP4P-Ew and see if they are affected.</div><div><br></div><div>David Mobley</div><div>Assistant Professor</div><div>Department of Chemistry</div><div>University of New Orleans<br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">January 29, 2009 4:21:41 AM CST</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>, <<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>>, <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>free energy with TIP4P bug fixed</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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: 0; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Hi,<br><br>The Coulomb energy difference that Chris Neale observed recently<br>was caused by a bug in the neighborlist assignment with the combination<br>of free energy and tip4p water optimization.<br>This bug would cause a few tip4p-tip4p charge interactions to be missing.<br>I think it has been present in all Gromacs version which have tip4p optimized loops,<br>for sure it was in 3.3.<br>I have fixed this for the upcoming Gromacs 4.0.4 release.<br><br>I assume this bug also caused the cut-off dependence that David Mobley observed.<br><br>I have done a lot of free energy calculation with tip4p and never noticed<br>any problems. This was because I always had the perturbed molecule<br>in a separate energy group, which circumvents the problem.<br><br>So for the moment and for checking if you had the problem with older Gromacs<span class="Apple-converted-space"> </span><br>versions, you can simply put the perturbed atoms and tip4p in separate energy groups.<br><br>Berk<br><br><br><hr>What can you do with the new Windows Live?<span class="Apple-converted-space"> </span><a href="http://www.microsoft.com/windows/windowslive/default.aspx" target="_new">Find out</a></div></span></blockquote></div><br></div></body></html>