[AMBER] error: "STOP PMEMD terminated abnormally"

From: Chinh Su Tran To <chinh.sutranto.gmail.com>
Date: Wed, 13 Aug 2014 03:06:48 -0400

Hi Amber users,

I found topic *STOP PMEMD Terminated Abnormally *on the mailing list, but
havent found the solution for my case. Could you please help take a look?

I have run MD simulation (85ns) for my model with an interval of 5ns for
each run.
I got "*STOP PMEMD Terminated Abnormally*!", and the output file gave me an

*ERROR: I could not understand line 29789*
*-327.9383128 54.8526179-268.4522643*

In the rst file, i.e. md80ns.rst, the line 29789 is shown as below:

*line29788: -327.4408536 55.5700723-268.8447251-327.5749078
*line29789: -327.9383128 54.8526179-268.4522643*
*line29790: -0.1930019 -0.1454533 -0.1407440 -0.0039895 -0.4009776

I have no idea what causes the problem here because the format (6 columns
or 3 columns in the line 29789) is similar to other successful files (e.g.

My md.in is as below:

* imin=0,*
* irest=1,*
* ntx=7,*
* ntb=2,*
* pres0=1.0,*
* ntp=1,*
* taup=2.0,*
* cut=10.0,*
* ntr=0,*
* ntc=2,*
* ntf=2,*
* tempi=300.0,*
* temp0=300.0,*
* ntt=3,*
* gamma_ln=1.0,*
* nstlim=2500000,*
* dt=0.002,*
* ntpr=2500,*
* ntwx=2500,*
* ntwr=2500*
* /*

By the way, it happened once before (e.g. to the file md70ns.rst), but when
I repeated the run on another machine, it was fine. And with this machine,
it occurs as mentioned above.

Please help.
Thank you very much.

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Received on Wed Aug 13 2014 - 00:30:02 PDT
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