<div dir="ltr">Hi,<div><br></div><div>Historically we have twisted the meaning of "integrator" as an .mdp file setting to include normal mode and energy minimization calculation. Those don't make sense to couple with replica exchange. So inasmuch as there is a Markov Chain that makes sense to generalize across ensembles in your approach, feel free to make the logic leading to that message tolerate however you are setting up your inputs.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Jun 7, 2018 at 5:34 PM Michael R Shirts <<a href="mailto:Michael.Shirts@colorado.edu">Michael.Shirts@colorado.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">> 1. Would a MC simulation, where moves are randomly chosen and accepted according to Metropolis criterion, be considered random integration?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">> 2. Is there something theoretical that disqualifies random integrators from parallel tempering, or are they simply not supported by
GROMACS at this time?<u></u><u></u></span></p>
<p class="MsoNormal">There is no issue with performing parallel tempering with Metropolis Monte Carlo. Parallel tempering simply allows exchange between systems that are sampling from equilibrium distributions. It can be used with any such simulations, no
matter the type. Different types of sampling might require different implementations of the same math, though. I think “dynamical” simulation just means one simulation is carrying out sampling, not doing something else. Perhaps the error could be a bit clearer.<u></u><u></u></p>
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<p class="MsoNormal"><span style="color:black">Best,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">~~~~~~~~~~~~~~~~<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">Michael Shirts<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">Associate Professor<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black"><a href="mailto:michael.shirts@colorado.edu" target="_blank"><span style="color:#0563c1">michael.shirts@colorado.edu</span></a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black"><a href="http://www.colorado.edu/lab/shirtsgroup/" target="_blank"><span style="color:#0563c1">http://www.colorado.edu/lab/shirtsgroup/</span></a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">Phone: (303) 735-7860<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">Office: JSCBB C123<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">Department of Chemical and Biological Engineering<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:black">University of Colorado Boulder<u></u><u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>> on behalf of Gregory Schwing <<a href="mailto:go2432@wayne.edu" target="_blank">go2432@wayne.edu</a>><br>
<b>Reply-To: </b>"<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<b>Date: </b>Thursday, June 7, 2018 at 9:11 AM<br>
<b>To: </b>"<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers@maillist.sys.kth.se</a>" <<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers@maillist.sys.kth.se</a>><br>
<b>Subject: </b>[gmx-developers] Elaboration of the error message "Replica exchange is only supported by dynamical simulations"<u></u><u></u></span></p>
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<p><span style="font-size:12.0pt;color:black">Dear GMX-Dev Mailing List:<u></u><u></u></span></p>
<p><span style="font-size:12.0pt;color:black"><u></u> <u></u></span></p>
<p><span style="font-size:12.0pt;color:black">I am interested in adding parallel tempering to a Monte Carlo simulation engine known as GOMC. Naturally, I am using the GROMACS implementation as a guide. However, GOMC is not an MD engine, so I was concerned
when I read the error message noted in the subject of the email, found in repl_ex.cpp. My question is twofold:<u></u><u></u></span></p>
<p><span style="font-size:12.0pt;color:black"><u></u> <u></u></span></p>
<ol start="1" type="1">
<li class="MsoNormal" style="color:black">
<span style="font-size:12.0pt">Would a MC simulation, where moves are randomly chosen and accepted according to Metropolis criterion, be considered random integration?<u></u><u></u></span></li><li class="MsoNormal" style="color:black">
<span style="font-size:12.0pt">Is there something theoretical that disqualifies random integrators from parallel tempering, or are they simply not supported by GROMACS at this time?<u></u><u></u></span></li></ol>
<p><span style="font-size:12.0pt;color:black"><u></u> <u></u></span></p>
<p><span style="font-size:12.0pt;color:black">Sincerely<u></u><u></u></span></p>
<p><span style="font-size:12.0pt;color:black"><u></u> <u></u></span></p>
<p><span style="font-size:12.0pt;color:black">Greg<u></u><u></u></span></p>
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