<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br>Hi, <br><br>I tried to compare PME and PME-switch for a small peptide in solution with Amber96. I was surprised to see that when introducing the Switch function, only the real-space energy is affected, whereas the reciprocal-space part is not. The difference in total energy is huge, about 4919 kJ/mol for my system. Below are the numbers. Shouldn't the reciprocal energy be "switched" as well, in the spirit of what the error function does in Eq. (4.160) and (4.161) of the 4.6.1 manual?<br><br>Unfortunately, the energy is not just shifted by a constant. Comparing two different conformations with PME and PME-Switch gives me a DeltaDeltaE of the order of 58 kJ/mol. I also compared the energies with Amber12, and found that PME reproduced the Amber electrostatics within 21 kJ/mol, with a DeltaDeltaE below 2 kJ/mol comparing the two conformations in gromacs and Amber12.<br><br>I ran extensive simulations of this peptide with gromacs 4.5.5 and PME-Switch (using various enhanced sampling methods). The peptide would never stay folded, whereas it has been reported to have a significant folded population in simulations with the same force field and cutoffs done with the Amber8 package. Do you think this could be due to the altered electrostatics? I can't see any other explanation at the moment. <br><br><br>Gromacs 4.5.5 PME :<span class="Apple-tab-span" style="white-space:pre"> </span><br>Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>2898.323974<br>Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre"> </span>-221730.3613<br>Coul. recip.<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.81872<br>Potential<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-204582.3431<br> <span class="Apple-tab-span" style="white-space:pre"> </span> <br>Gromacs 4.5.5 PME-Switch :<span class="Apple-tab-span" style="white-space:pre"> </span><br>Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>2898.323974<br>Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre"> </span>-226649.5443<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>difference = -4919.1830<br>Coul. recip.<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.81872<br>potential<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-209501.5261<br> <span class="Apple-tab-span" style="white-space:pre"> </span> <br>Gromacs 4.6.1 PME, coulomb-modifier=none<br>Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>2898.32373<br>Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre"> </span>-221730.4063<br>Coul. recip.<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.46875<br>potential<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-204592.1719<br><br>Gromacs 4.6.1 PME-switch, coulomb-modifier=none<br>Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>2898.32373<br>Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre"> </span>-226649.625<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>difference = -4919.2188<br>Coul. recip.<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.46875<br>potential<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>-209511.3906<br><br><br>I can send files and more elaborate data if required.<br><br>Thanks and kind regards,<br>Michel<br><br><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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