AMBER Archive (2009)

Subject: [AMBER] Problem on PMEMD

From: zyxism (zyxism_at_gmail.com)
Date: Mon Sep 14 2009 - 20:11:57 CDT

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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