<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 14px; border-collapse: collapse; color: rgb(34, 34, 34); "><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 14px; border-collapse: collapse; color: rgb(34, 34, 34); ">dear teacher,</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 14px; border-collapse: collapse; color: rgb(34, 34, 34); ">i find the answer of that letter "</span>Subject: Re: [gmx-users] REMD: NPT being +-Infinity or NaN",</div>
<div>ifind that "when the exchange, the temperature abruptly surge .",as follows,</div><div>dt=0.002ps -replex 4000</div><div><br></div><div><div>@ s0 legend "Temperature"</div><div>@ s1 legend "Pressure"</div>
<div> 0.000000 546.497375 60.637791</div><div> 1.000000 556.582397 244.328201</div></div><div>......</div><div><div> 94.000000 557.564453 -17.035589</div><div> 95.000000 543.882629 57.111996</div><div>
96.000000 523.336548 -25.745819</div><div> 97.000000 555.043335 254.709778</div><div> 98.000000 555.595886 -39.830761</div><div> 99.000000 542.395325 49.084045</div><div> 100.000000 550.955261 -149.259979</div>
<div> 101.000000 134372.953125 4419.518066</div><div> 102.000000 156382.859375 -17109.099609</div><div> 103.000000 138660.156250 -11395.237305</div><div> 104.000000 165148.265625 20807.541016</div></div><div>.......</div>
<div><br></div><div>But if change the replex to 400000000,so i can not exchange.</div><div>Then the system is ok.</div><div>&& The initial conformation has been done a long time MD</div><div><br></div><div>thanks for your help !!</div>
<div><div>Bo Du</div><div>Department of Polymer Science and Engineering,</div><div>School of Chemical Engineering and technology,</div><div>Tianjin University, Weijin Road 92, Nankai District 300072,</div><div>Tianjin City P. R. China</div>
<div>Tel/Fax: +86-22-27404303 ; +8613820062885</div><div>E-mail: <a href="mailto:2008dubo@gmail.com">2008dubo@gmail.com</a> ; <a href="mailto:dubo2008@tju.edu.cn">dubo2008@tju.edu.cn</a></div></div><div><br></div><div><br>
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Message: 4<br>Date: Sun, 27 Nov 2011 22:36:08 -0500<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" style="color: rgb(17, 85, 204); ">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] REMD: NPT being +-Infinity or NaN<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" style="color: rgb(17, 85, 204); ">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4ED301A8.9070609@vt.edu" style="color: rgb(17, 85, 204); ">4ED301A8.9070609@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br><br><br><br>¶Å²¨ wrote:<br>> dear teacher,<br>> when i do remd in the npt ensemble.<br>><br>> REMD: NPT -replex 4000<br>> dt= 0.0001<br>><br>> step 172000, will finish Sat Dec 31 18:44:12 2011<br>
><br>> -------------------------------------------------------<br>> Program mdrun_mpi_4.5.5, VERSION 4.5.5<br>> Source code file: nsgrid.c, line: 549<br>><br>> Range checking error:<br>> Explanation: During neighborsearching, we assign each particle to a grid<br>
> based on its coordinates. If your system contains collisions or parameter<br>> errors that give particles very high velocities you might end up with some<br>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>
> put these on a grid, so this is usually where we detect those errors.<br>> Make sure your system is properly energy-minimized and that the potential<br>> energy seems reasonable before trying again.<br>><br>
> how could i do except using the small dt ?<br>><br><br>Your system is not stable, as is often the case with NPT REMD at high temperature.<br><br><a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up" target="_blank" style="color: rgb(17, 85, 204); ">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>-Justin<br><br>--<br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank" style="color: rgb(17, 85, 204); ">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank" style="color: rgb(17, 85, 204); ">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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