<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Berk,<div><br></div><div>Any chance of getting a fix for 3.3.x versions also? I have several papers which probably are affected by this problem and I will need to repeat the calculations with a fixed version and produce errata. I would prefer to do this with 3.3.x since (a) not all of the data is with TIP4P, and so I don't need to repeat all the calcs, and would like to use a consistent version, and (b) I am not sure that 4.x does not introduce additional bugs that might affect my calcs.</div><div><br></div><div>Thanks!</div><div>David</div><div><br><div><div>On Jan 29, 2009, at 4:21 AM, Berk Hess 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: 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>