AMBER Archive (2007)

Subject: RE: AMBER: bug in reprocessing with PB?

From: Ray Luo (rluo_at_uci.edu)
Date: Thu May 10 2007 - 16:04:42 CDT

David,

Please give me one month to fix the bug ... I'm teaching two classes this
quarter.

Best,
Ray

==========================================
Ray Luo, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900
Phone: (949) 824-9528
Email: rluo_at_uci.edu
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
David Mobley
Sent: Thursday, May 10, 2007 12:20 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: bug in reprocessing with PB?

Dear Ray,

> This is a known bug in imin=5 with the PB module. A likely place is the
> memory allocation and re-initialization routine. We are looking into this
as
> well in our own applications.

Ahh, glad to hear I'm not the only one having problems. Do you guys
have a rough estimate on timeframe? (i.e., if it's an issue of a few
days/couple weeks, I'll wait, but if it's a month or more, I'll find
some other way to do what I'm trying to do).

Thanks,
David

> All the best,
> Ray
> ==========================================
> Ray Luo, Ph.D.
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900
> Phone: (949) 824-9528
> Email: rluo_at_uci.edu
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
> -----Original Message-----
> From: David A. Case [mailto:case_at_scripps.edu]
> Sent: Thursday, May 10, 2007 11:24 AM
> To: amber_at_scripps.edu
> Cc: rluo_at_uci.edu
> Subject: Re: AMBER: bug in reprocessing with PB?
>
> On Thu, May 10, 2007, David Mobley wrote:
>
> > However, I'm attaching a tarball for one case that fails
> > (with PB) on either architecture. Again, it reprocesses fine using GB.
>
> Nothing was attached(!?!).
>
> Ray: if you or your people can look at this, it would be great: we need to
> make the pb routines in sander more reliable...thx
>
> ...dac
>
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