[gmx-users] MD run end abnormally

主月 :) jiqing at iccas.ac.cn
Mon Jul 3 03:27:39 CEST 2006

Hi :
Mark, thanks for your advice.
But i only use the single-processor.And the enviourment is RedHat 9.0 with gromacs 3.3.1.

And if i just use mdrun -v, the process goes well. if i use mdrun -v >& output&, the problem will occur.

what is other problem of this error
Date: Sun, 2 Jul 2006 15:17:53 +1000 (EST)
From: "Mark Abraham" <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] MD run end abnormally
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
<2028. at sqmail.anu.edu.au>
Content-Type: text/plain;charset=iso-8859-1

> Hi:
> I install GMX FFTW MPI in my own folders. And then i used a begin
> structure which performed well at other computers to test the GMX
> programme.
> What is strange to me is that the job can run well at begginning time but
> after a while the CPU was not still busy, and the output file was not
> change. I chencked the log file. There is no reason. And i used g_energy
> to check the condition of  MD.But the "Potential"Kinetic En."
> "Temperature" were all in equilibrium.
> Every time the error came with different step. Some time is 50000 step.
> Some time is 2445001 .
> What is the error? How can i fix it.

It sounds like you are using a Windows MPI environment that isn't working
properly. Test single-processor calculations to see they work OK. If so,
try to eliminate other processes running on the machines, and turn off any
auto-hibernation stuff.



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