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On 12/27/2011 7:44 PM, lina wrote:
<blockquote cite="mid:4EF9855B.2000500@gmail.com" type="cite">Hi,
<br>
<br>
<br>
I met a very untamed simulation system.
<br>
<br>
when I tried to run a short MD, it's collapsed with LINCS
Warnings, It's under 317K
<br>
<br>
so I used energy minimizations after NVT, and run another NVT_2
again. (In vacuum, no NPT being applied here).
<br>
<br>
after that NVT_2, mainly increased the steps, run MD, it's
collapsed again after 500ps,
<br>
<br>
so I used the energy minimization from that nvt_2.gro several
times, and it's collapsed during energy minimizations.
<br>
<br>
Might I used wrong way of handling it. I tried 300K, which can run
a bit further without collapse.
<br>
<br>
Thanks for any suggestions you may give.
<br>
<br>
Do I need to work hard on the energy minimization or?
<br>
</blockquote>
<br>
The usual advice is here <a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>.<br>
<br>
Mark<br>
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