AMBER Archive (2009)

Subject: Re: [AMBER] Problem on PMEMD

From: Tom Joseph (
Date: Mon Sep 14 2009 - 20:34:11 CDT

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


2009/9/14 zyxism <>:
> 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
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