Hi Myunggi
I looked at the code and found where this happens. The wrapped crds are in
a temp array, but the binary write occurs from the regular coordinate array.
It's an easy fix I can put in 10, maybe even issue a patch too for 9.
Thanks for reporting this.
Best Regards - Bob
----- Original Message -----
From: "Myunggi Yi" <myunggi.gmail.com>
To: <amber.scripps.edu>
Sent: Wednesday, November 14, 2007 2:18 PM
Subject: AMBER: Bug report: iwrap failure in PMEMD with netCDF
> Dear Amber users,
>
> I found a bug.
> I have reported the iwrap failure in pmemd,
> and the problem has been solved with the patch.
>
> However, when I run with "ioutfm=1" (netCDF format for the trajectory),
> I reproduce the same problem (water molecules get out of the primary
> unit cell) as before the bug fix.
> The patch works with only formatted output (this works fine with the
> restart file also).
>
> I used 16 cpus on a linux cluster with intel mpich2 (infiniband).
>
> I hope this help fix the bug and the release of amber 10.
> Have a nice day.
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
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Received on Sun Nov 18 2007 - 06:07:15 PST
