AMBER Archive (2007)

Subject: AMBER: Bug report: iwrap failure in PMEMD with netCDF

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Nov 14 2007 - 13:18:18 CST

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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