AMBER Archive (2009)

Subject: Re: [AMBER] Problem on PMEMD

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Mon Sep 14 2009 - 20:40:35 CDT

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_at_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
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
                            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_at_qtp.ufl.edu

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber