AMBER Archive (2003)

Subject: Re: run sander?

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 02 2003 - 12:52:00 CDT

On Mon, Jun 02, 2003, quch quch wrote:

> I have problem to run sander on test file, could
> anyone tell me what is wrong with the input file?
>
> Input file ($AMBERHOME/test/vac_rna):
>
> mpirun -np 1 sander -O -i gbin -c md4.x -o test.out
>
> Output has errors like this:
> =============================
> 1. RESOURCE USE:
>
>
> EWALD SPECIFIC INPUT:
>
> | Using the SGI specific (ZFFT3D) Fast Fourier
> Transform
> | Using the T3D specific (FFT3D0) Fast Fourier
> Transform
> Largest sphere to fit in unit cell has radius =
> 0.000
>
> Ewald PARAMETER RANGE CHECKING:
> parameter skinnb+cutoffnb: (nonbond list cut) has
> value 0.10000E+03
> This is outside the legal range
> Lower limit: 0.00000E+00 Upper limit: 0.00000E+00
> Check ew_legal.h
> ============================
>

This is weird. You can look at the sample output, mdout.min.save, and compare
it to yours. It should not have anything like "EWALD SPECIFIC INPUT" in
the output, and having it say that you are using both SGI and T3D FFT's
seems odd.

What machine are you running on? Which MACHINE file did you use? If you
can't figure anything out, please post the complete output file.

Is there any chance that the "sander" in your path is actually amber6 sander
rather than amber7 sander? (Type "which sander" to see what you are getting.)

..regards...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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