[gmx-users] Fwd: (A problem with GROMACS)

Tsjerk Wassenaar tsjerkw at gmail.com
Fri May 12 11:12:30 CEST 2006

Hi Jahanshah,

Please keep these discussions on the list.., they may be of use to others.

First, you have to make sure that the restart was due to gromacs and not
some other source. If the log-file doesn't show any errors, it could have
been due to something else. Try to run your simulation again, starting from
the last frame in the .trr file, and see if the same thing happens again. If
it does, you can try to take that frame and set it up again with a modified
.mdp, where you don't generate velocities. In addition, write to the energy
file at every step. Then you can see whether before the crash there are
sudden increases in one of the terms.

Good luck,


---------- Forwarded message ----------
From: jahanshah ashkani <ashkani_2003 at yahoo.com>
Date: May 11, 2006 5:37 PM
Subject: (A problem with GROMACS)
To: tsjerkw at gmail.com

Daer professor Wassenaar,
Thanks for your reply. After 40000 steps my PC restarted, automaticly. But
there wasn't any error in log file. My PC is P4: CPU=2.4 Full, RAM=1G,
Mainboard=MSI 865 p neo, HDD=80 plus and I ran GROMACS3.2 on WindowsXP.
Thank you very much.

Sincerely yours,
Jahanshah Ashkani

Yahoo! Messenger with
calls for ridiculously low rates.


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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