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On 28/11/2011 10:37 PM, 杜波 wrote:
<blockquote
cite="mid:CAAH6B-=+ba2tCsKNJ3ktyBxOFZ5mRMO_MA0o5cEtuWSmK4NGPg@mail.gmail.com"
type="cite"><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>
</span></blockquote>
<br>
If this is the same system as previously reported, then you're
probably observing the system velocities exploding on one replica
then being exchanged to a new replica.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAH6B-=+ba2tCsKNJ3ktyBxOFZ5mRMO_MA0o5cEtuWSmK4NGPg@mail.gmail.com"
type="cite"><span class="Apple-style-span" style="font-family:
arial, sans-serif; font-size: 14px; border-collapse: collapse;
color: rgb(34, 34, 34); ">
<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 moz-do-not-send="true"
href="mailto:2008dubo@gmail.com">2008dubo@gmail.com</a> ;
<a moz-do-not-send="true" href="mailto:dubo2008@tju.edu.cn">dubo2008@tju.edu.cn</a></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><font class="Apple-style-span" size="3"><span
class="Apple-style-span" style="font-size: 11px; "><br>
</span></font></div>
<div><font class="Apple-style-span" size="3"><span
class="Apple-style-span" style="font-size: 11px;"><br>
</span></font></div>
<div><font class="Apple-style-span" size="3"><span
class="Apple-style-span" style="font-size: 11px;"><br>
</span></font></div>
<div>=======================================================================================================</div>
Message: 4<br>
Date: Sun, 27 Nov 2011 22:36:08 -0500<br>
From: "Justin A. Lemkul" <<a moz-do-not-send="true"
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
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org"
style="color: rgb(17, 85, 204); ">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
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>
杜波 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 moz-do-not-send="true"
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 moz-do-not-send="true" href="http://vt.edu/"
target="_blank" style="color: rgb(17, 85, 204); ">vt.edu</a> |
(540) 231-9080<br>
<a moz-do-not-send="true"
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>
</span>
<br>
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</blockquote>
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