Dear GMX-Developers and Shirts, <div><br></div><div>To reproduce the the problem, I use the material in GROMACS Tutorials <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html" target="_blank">Lysozyme in Water</a>.<br></div><div><br></div><div>Yes, Prof. Shirts. If I use standard vdwtype=cut-off, coulombtype=pme and cutoff-scheme=group, the simulation temperature accords with the ref_t.</div><div>If I use gromos ff and tabulized potential, there is no temperature problem.</div><div><br></div><div>Now the problem is pinned on the relation between tabulized potential and thermostat under amber99sb-ildn ff.</div><div><br></div><div>I filed Bug #2286 in redmine.</div><div>https://redmine.gromacs.org/issues/2286</div><div><br></div><div>Hope you could give some advice about this issue.</div><div><br></div><div>Yu</div><div><br><blockquote name="replyContent" class="ReferenceQuote" style="padding-left:5px;margin-left:5px;border-left:#b6b6b6 2px solid;margin-right:0">-----Original Messages-----<br>
<b>From:</b><span id="rc_from">"Michael R Shirts" <Michael.Shirts@Colorado.EDU></span><br>
<b>Sent Time:</b><span id="rc_senttime">2017-10-23 19:43:38 (Monday)</span><br>
<b>To:</b> "gmx-developers@gromacs.org" <gmx-developers@gromacs.org>, GMX-developer <gromacs.org_gmx-developers@maillist.sys.kth.se><br>
<b>Cc:</b> <br>
<b>Subject:</b> Re: [gmx-developers] Group cutoff-scheme simulation temperature affected by nh-chain-length<br><br>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">If you can file a bug report in redmine (<a href="http://redmine.gromacs.org/)" target="_blank">http://redmine.gromacs.org/)</a> with example files, that would be useful. Before you file it can you check
if problem happens if you use standard cutoffs, instead of tabulated cutoffs? I wonder if there is some sort of code path that it’s going down. I will bet that combination of inputs has only very rarely been used. Also, you said the temperature jumps. Does
it come back down to 310, or does it stay 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">Generally, I would recommend using v-rescale instead of Nose-Hoover. Nose-Hoover has some known flaws; increasing the chain length is supposed to help things, but doesn’t really help that
much for realistic systems, just with very simple ones.<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">However, any Nose-Hoover change length should in principle give the same average, and did when the code was written. If it doesn’t, the code was broken somewhere, possibly because of lack
of coverage in the regression tests and something getting out of sync.<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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Associate Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><a href="mailto:michael.shirts@colorado.edu" target="_blank"><span style="color:blue">michael.shirts@colorado.edu</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black"><a href="http://www.colorado.edu/lab/shirtsgroup/" target="_blank"><span style="color:blue;text-decoration:none">http://www.colorado.edu/lab/shirtsgroup/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Phone: (303) 735-7860<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;color:black">Office: JSCBB C123<o:p></o:p></span></p>
<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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;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 "Du, Yu" <<a href="mailto:duyu@sioc.ac.cn" target="_blank">duyu@sioc.ac.cn</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>Monday, October 23, 2017 at 12:48 AM<br>
<b>To: </b>GMX-developer <<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] Group cutoff-scheme simulation temperature affected by nh-chain-length<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">Dear GMX Developer and Prof. Hess, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I think this question is not common to GMX users, so I post it here.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Prof. Hess is very familiar with the tabulized potential and group cutoff scheme, so I also CC this email to you. <span style="font-size:10.5pt">Any advice will be appreciated. </span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The Backgroud:<o:p></o:p></p>
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<p class="MsoNormal">I simulated protein-ligand system (ref_t=300) with amber99sb-ildn ff. <span style="font-size:10.5pt">I used the normal table6-12.xvg tabulized potential to reproduce this problem.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The Problem:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">In NVT simulation, integrator=md-vv, Tcoupl=nose-hoover, </span>coulombtype=pme-user, vdwtype=user<span style="font-size:10.5pt">. I found that at the start of the simulation, there is a temperature jump to
around 310K (average 310K in 100ps) higher than the ref_t (300K) under nh-chain-length=10.</span><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 tuned and spotted the nh-chain-length parameter. If I used nh-chain-length=1 there is no temperature jump and temperature can converge very well to 300K.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">2)I replicated the same experiment in verlet scheme, the temperature converged to ref_t 300K in 100ps and no jump in <span style="font-size:10.5pt">nh-chain-length=2, which can 50K temperature jump (to 350K).</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The Question:<o:p></o:p></p>
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<p class="MsoNormal">1)How will the <span style="font-size:10.5pt">nh-chain-length parameter affect the simulation temperature under the group cut-off scheme?</span><o:p></o:p></p>
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<p class="MsoNormal">2)Is it valid to use NH (<span style="font-size:10.5pt">nh-chain-length=1) not NH chain (nh-chain-length>1) to simulate the protein-ligand system?</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">Thanks for any advice.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">--</span><o:p></o:p></p>
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<p class="MsoNormal">Du, Yu<br>
PhD Student,<br>
Shanghai Institute of Organic Chemistry <o:p></o:p></p>
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<p class="MsoNormal">345 Ling Ling Rd., Shanghai, China. <o:p></o:p></p>
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<p class="MsoNormal">Zip: 200032, <span style="font-size:10.5pt">Tel: (86) 021 5492 5275</span></p></div></div></div></div></blockquote></div>