AMBER Archive (2009)

Subject: Re: [AMBER] Energy minimisation and NaN

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Apr 13 2009 - 14:28:10 CDT

On Mon, Apr 13, 2009, vivek.viv.sharma_at_gmail.com wrote:

> I am using the command
>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
> mpirun -np 4 /usr/local/amber10/exe/sander.MPI -O -i minimise.in -o
> minimise.out -c final_12S.inpcrd -p final_12S.prmtop -r final_12S.rst
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>
> It showed the following error:
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
> One of the processes started by mpirun has exited with a nonzero exit
> code. This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>
> PID 3933 failed on node n0 (127.0.0.1) due to signal 11.
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>
> After checking the "minimise.out" file, I observed the following details
> in it:
>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 4.0063E+15 N 1792
> BOND = 16082.1321 ANGLE = 10271.7354 DIHED = 9025.5857
> VDWAALS = NaN EEL = NaN HBOND = 0.0000
> 1-4 VDW = 3502.0741 1-4 EEL = 27317.6570 RESTRAINT = 0.0000

It looks like you probably have two atoms nearly on top of each other.
To debug:

1. Run a short (10 step) minimization with ntpr=1 and a serial job.
That will help establish whether or not this is a serial/parallel
problem, or something related to the initial structure.

2. use the "checkoverlap" command in ptraj to look for bad contacts in
your structure. You may have to fix these before proceeding.

...dac

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