AMBER Archive (2003)

Subject: Re: AMBER: input/output error

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Fri Oct 10 2003 - 17:10:08 CDT

Hello,

Have you checked that the output device has available space
via UNIX command df ?
If Fortran records are ~1k then ~260Mb have been consumed by
step 17000; another 93000 steps will result in ~1.5Gb.
As recently mentioned by Yong Duan, a 1 or 2 ps output frequency
is usually sufficient; see google search:
output frequency site:structbio.vanderbilt.edu

So ntwx=1000 is recommended.

Scott

On Fri, 10 Oct 2003, Dalmaris, John wrote:

> Hello All,
>
> I am running dynamics using DMSO solvent by applying belly to a small
> peptide. It is running without any problem when at after 17000 steps it
> stops writing in the out file.
>
> There is the following error message:
>
> Input/Output Error 173: Input/output error
>
> In Procedure: corpac
> At Line: 55
>
> Statement: Formatted WRITE
> Unit: 12
> Connected To: md_pept_DMSO_bellynew.crd
> Form: Formatted
> Access: Sequential
> Records Read : 0
> Records Written: 267809
>
> Current I/O Buffer:
>
> 20.924 23.656 18.163 22.578 22.881 17.952
> !
>
>
> End of diagnostics
>
> The input file is as follows:
> &cntrl
> imin=0, ntx=1, nmropt=1,
> ntwr=1000, ntwx=100,
> ntf=2, ntb=2, cut=12.0, ibelly=1,
> nstlim=100000, dt=0.001,
> temp0=300.0, tempi=0.0, ntt=1,
> ntp=1, taup=2.0, npscal=1,
> ntc=2,
> &end
> &wt
> type='TEMP0', istep1=0, istep2=10000,
> value1=0.0, value2=300.0,
> &end
> &wt
> type='TEMP0', istep1=10001, istep2=100000,
> value1=300.0, value2=300.0,
> &end
> &wt
> type='END',
> &end
> &rst
> iat=0,
> &end
> #Hold the peptide fixed
> RES 9 514
> END
> END
>
> Does anyone know why data stopped rolling into the out file?
> Thank you very much for your help
>
> Best wishes,
>
> John
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