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On 28/04/2012 4:14 PM, Albert wrote:
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hello Mar:<br>
thanks a lot for kind reply.<br>
From the link you you mentioned, it seems that this problem
comes from the MD system itself. However, it goes well in my
workstation. Moreover, I visualized and analyzed the results from
my workstation running, everything goes well. I don't find any
problem with it.<br>
<br>
But I don't know why it doesn't work in the blue gene computer.<br>
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Sometimes a marginally stable calculation will work or not based on
apparently insignificant things, like whether it's in parallel or
not. Numerical integration can be messy. If you prepare the system
slightly better and/or equilibrate more gently, then it will run
under BlueGene, from your evidence of what I assume to be "lucky"
good behaviour on your workstation.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4F9B8AA9.9050506@gmail.com" type="cite"> <br>
THX<br>
<br>
ALbert<br>
<br>
<br>
<br>
On 04/28/2012 07:36 AM, Mark Abraham wrote:
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On 28/04/2012 2:04 PM, Albert wrote:
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<font size="+1"><font face="Arial">hello:<br>
I am running NPT on a blue gene cluster, but the jobs
always failed with following messages. However, everything
goes well if I run it on my local cluster:</font></font><br>
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Systems with marginally stable initial conditions can do this.
See <a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps">http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps</a>.<br>
<br>
Mark<br>
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