Re: job termination

From: Chris Harrison (
Date: Fri Feb 11 2011 - 11:50:20 CST

You need to cut and paste the text directly into the message. Attaching
doc formats doesn't work well with the archives, making it difficult for
future users with the same problem.

Without more to go on, you're likely experiencing a system instability.
Your best approach will be to rerun the last 10-100 steps of the
2ns-timestep run but with a dcdfreq of 1, and then visualize the
simulation backwards to discern the beginnning of the instability.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 217-244-1733              Fax:   217-244-6078
ipsita basu <> writes:
> Date: Fri, 11 Feb 2011 12:16:17 +0530
> From: ipsita basu <>
> To: namd-l <>
> Subject: namd-l: job termination
> Hi all,
>          I have a problem running namd.
>          I minimized my system for 200000 steps, I equilibrate the
> system using timestep 1fs/step and the job is running without giving
> any problem. But during production run when I use 2fs timestep, the
> job is terminated frequently after 20 or 30 ps fiving error :
> ERROR: Constraint failure in RATTLE algorithm for atom 38767!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
> I check the system in vmd, everything is ok. If I again restart the
> from that point agin it starts running and is terminated after few ps.
> I observe a test run using timestep 1fs, no such problem occures.
> My input is attached herewith.
> Can anyone please help me.
> Thank you.
> -- 
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009

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