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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">I’ll raise the issue on the amber developer list about the provenance of the parameters there.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">~~~~~~~~~~~~~~~~<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Michael Shirts<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Department of Chemical and Biological Engineering<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">University of Colorado Boulder</span><span style="font-size:11.0pt;font-family:Calibri"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black"><gromacs.org_gmx-developers-bounces@maillist.sys.kth.se> on behalf of Erik Lindahl <erik.lindahl@gmail.com><br>
<b>Reply-To: </b>"gmx-developers@gromacs.org" <gmx-developers@gromacs.org><br>
<b>Date: </b>Monday, May 29, 2017 at 1:45 AM<br>
<b>To: </b>"gmx-developers@gromacs.org" <gmx-developers@gromacs.org><br>
<b>Subject: </b>Re: [gmx-developers] high-precision TIP3P parameters?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi, <o:p></o:p></p>
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<p class="MsoNormal">I think Igor has a point that we should make our implementation of Amber as accurate as possible, but let's make sure we only change things once.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">There has also been at least once instance where Amber changed they way they defined improper torsions internally without documentation, so we went from perfect matches in Amber ~8 to mismatching, and then back to matching.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">1. I agree the Amber implementation should be our reference for Amber, but do the parameter files in the Amber package match the published force field exactly? Let's double-check that paper.<o:p></o:p></p>
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<p class="MsoNormal">2. This If we should change, I would suggest making a quick audit of _all_ our Amber parameters and see if there are more rounding errors/deviations. If so, let's change all of them at the same time.<o:p></o:p></p>
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<p class="MsoNormal">3. I also agree with Berk that this is only worth doing if we really get everything to match pretty close to perfectly. It's better to have a known insignificant discrepancy than a set of parameters that keeps changing!<o:p></o:p></p>
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<p class="MsoNormal">Cheers,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Erik<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, May 29, 2017 at 9:36 AM, Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi, <o:p></o:p></p>
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<p class="MsoNormal">My opinion is that we should minimize the number of time we change force field parameters, as this is confusing for users. The difference here is very small and the Coulomb constant also differs from Amber. I would only want to change this
when we can get the total energy to match the Amber code up to all decimals.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Berk<o:p></o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">Erik Lindahl <<a href="mailto:erik.lindahl@gmail.com" target="_blank">erik.lindahl@gmail.com</a>><o:p></o:p></p>
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<p class="MsoNormal">Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University<o:p></o:p></p>
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<p class="MsoNormal">Science for Life Laboratory, Box 1031, 17121 Solna, Sweden<o:p></o:p></p>
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