And please please CHANGE the random seed for every restart !
Adrian
Tom Joseph wrote:
> This is an MPI error message, not a pmemd error message. You need to
> look at the mdout file (the file you specified with the -o option to
> pmemd) for error messages that will help you determine what happened
> here.
>
> --Tom
>
> 2009/9/14 zyxism <zyxism.gmail.com>:
>> Dear Amber,
>> I'm a new subscriber of this mail list.
>> When I did Nucleic Acid Simulation with PMEMD, using ff99 forcefield(modified with bsc0 and ion parameters ionsjc_tip3p),I made 300 scripts , 0.1ns each. But when the simulation was prolonged to about 15ns, the simulation was stopped, and the system message was like this :
>> rank 0 in job 271 local.localdomain 56517 caused collective abort of all ranks
>> exit status of rank 0:killed by signal 9
>> Is there something wrong with my scripts or with the use of forcefield?
>> Zheng
>>
>>
>>
>>
>> zyxism
>> 2009-09-15
>> _______________________________________________
>> AMBER mailing list
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>>
>
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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Mon Sep 14 2009 - 19:00:03 PDT
