[AMBER] AMBER11, pmemd.cuda: the system crashed.

From: Chinh Su Tran To <chinh.sutranto.gmail.com>
Date: Tue, 6 Dec 2011 11:33:22 +0800

Dear AMBER users,

I was running pmemd.cuda using Amber11 on a GPU which is installed in a
The process was of 2 steps of short minimizations and a 6ns of heating the
protein (270 residues) at 500K.

The minimizations were fine, but when i ran the heating, my system
"crashed". The errors are as below:

*[2932683.628873] EXT4-fs (sda1): previous I/O error to superblock detected*
[2932683.646789] EXT4-fs (device sda1): ext4_find_entry:933: inode#9699494:
comm init: reading directory lblock 0**
I re-booted the system, and tried to run it again. The same errors came.
My input file is:

* iwrap=1 => I also tried iwrap=0*
  nstlim=3000000, dt=0.002,
  ntpr=1500, ntwx=1500,ntwr=1000
We tried to find out what was going on, but we did not know where the crash
came from?
Please help.

Thank you.

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Received on Mon Dec 05 2011 - 20:00:02 PST
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