AMBER Archive (2007)

Subject: Re: AMBER: LINMIN Failure vs Parallelization

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Thu Sep 13 2007 - 05:24:10 CDT

>Dear all,
>
>I am using amber9 on Linux (RHEL4) and Mac (OSX).
>Recently i minimized a protein, vth its substrates and ions bound to it, u
>sing parallel version of amber9 on RHEL 4 with 2 processors and got an error
>of LINMIN failure.
in LINUX we also got the error.
however, run smoothly in SGI300 until convergent.
>After this error the minimization had stopped.
>Then i transferred the same job on Mac with parallel version of sander
>using 4 processors.
>On Mac the minimization was smooth and finished without any LINMIN failures..
>*What could be the possible cause for this?*
>It might be regrding
>the architecture of the two machines but i want to know how has this
>been possible..
>i mean considering the different machines and different results!!
>Kindly shed some light on it....
>
>Thanks.
>

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