[gmx-users] Re: writing checkpoint

[Berk Hess]

Hi,

That is very strange.
If you did not set the -cpt option, mdrun should only write a checkpoint file
every 15 minutes, not every 5 seconds.

What kind of machine are you running on?

Berk


Date: Wed, 5 Nov 2008 06:58:33 -0500
From: xianghong001 at gmail.com
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Re: writing checkpoint

Thanks, Berk:
 
My log file actually stop somewhere since its size didn't change for a long time. 
Yes, looks like it keeps writing checkpoint info. 
I should continue the simulation since the other file looks reasonable. 
 
I didn't use option -cpt. 
Thanks. 

-Xianghong Qi

On Wed, Nov 5, 2008 at 6:39 AM, Berk Hess <gmx3 at hotmail.com> wrote:


Hi,

Why do the log file seem to stop?
It keeps writing checkpoint info, right?
So I assume it is still running fine.

But it seems you have selected checkpointing at (nearly) every step.
Did you use -cpt 0?

If you don't want checkpoints, you have to set -cpt -1.

Berk



Date: Wed, 5 Nov 2008 06:10:03 -0500
From: xianghong001 at gmail.com
To: gmx-users at gromacs.org

Subject: [gmx-users] Re: writing checkpoint 





Hello, all:
 
I got a message when I run my simulation: 
 
Writing checkpoint, step 100200 at Wed Nov  5 05:22:42 2008
Writing checkpoint, step 100210 at Wed Nov  5 05:22:46 2008
Writing checkpoint, step 100220 at Wed Nov  5 05:22:51 2008
Writing checkpoint, step 100230 at Wed Nov  5 05:22:55 2008
Writing checkpoint, step 100240 at Wed Nov  5 05:23:00 2008
.log file seems stop, but simulation is still running, and I can see
.xtc , .edr file are growing.  Does anyone has some idea about this
situation?  Thanks in advance. 
 
-Xianghong Qi
 
 
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