<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>Dear Berk,</div><div><br></div><div>Thanks for your immediate reply. And I apologize for not providing the relevant cutoffs. Indeed I had a long switching range. </div><div><br></div><div>OK Whow. So it is exactly as I feared, all my simulations are flawed. Being a big proponent of energy conservation, when 4.5 came out, I thought PME-switch was like the new state-of-the-art scheme (without properly checking what it was doing, my bad...). Now I realize that it is not. It is even quite wrong, as it probably introduces a sign reversal in the force around rcoulomb. As you mentioned, switching can be attained in a safe and consistent way using ewald_rtol. </div><div><br></div><div>It seems to me that the PME-switch option is very dangerous. As you suggest I think it should be deprecated or at least it should be accompanied with a serious warning. </div><div><br></div><div>Thanks for your help, </div><div>Michel</div><div><br></div><div><br></div><div>On Mar 6, 2013, at 7:34 PM, <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a> wrote:</div><blockquote type="cite"><div>Message: 4<br>Date: Wed, 06 Mar 2013 19:29:19 +0100<br>From: Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>><br>Subject: Re: [gmx-developers] PME-Switch vs. PME<br>To: Discussion list for GROMACS development<br><span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>Message-ID: <<a href="mailto:51378AFF.9020201@kth.se">51378AFF.9020201@kth.se</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br><br>You don't mention your, critical, cut-off parameters.<br>I guess you used a long switching range. The switch is only intended to <br>avoid<br>cut-off artifacts (and therefore does not act on the reciprocal).<br><br>Any switching function should only be applied over a very short range.<br>As with PME ewald_rtol is usually 10^-5, you don't really need the switch,<br>and if you do want to use it, you should switch over 0.05 nm or less.<br><br>But in 4.6 you can use exact cut-off's, either with the Verlet cut-off <br>scheme,<br>or at a high cost also with the group cut-off scheme. Thus PME-switch is <br>no longer needed<br>and we should deprecate it in 4.6.<br><br>Cheers,<br><br>Berk<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; font-size: medium; "><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-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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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-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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>==========================================================</div><div>Michel Cuendet, PhD</div><div>Molecular Modeling Group</div><div>Swiss Institute of Bioinformatics</div><div>CH-1015 Lausanne</div><div>Switzerland</div><div><a href="http://lausanne.isb-sib.ch/~mcuendet/">http://lausanne.isb-sib.ch/~mcuendet/</a></div><div>==========================================================</div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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