RE: Monitoring progress of an ongoing molecular dynamics simulation

From: Cosseddu, Salvatore (
Date: Fri Mar 07 2014 - 10:43:29 CST

Hi Ivan,

That's quite strange. What version of namd are you using? I've never experienced anything like that with namd2.8 and namd2.9.

What do you mean by "buffering the output in memory". Do you see the RAM usage increasing? How often does namd write in the log file? As far as I know, tail just follows the file descriptor and it should not theoretically create a conflict. Sometime checks and update your screen. Your kernel should be aware of what's going on to avoid clashes.

Are you sure you have redirected correctly the output? Is there something written in the log file? With tee you actually duplicate the output, and if the redirection ">" and "tail" don't work, piping to tee will not work either. Before trying it you should check whether your tail is broken, or you are redirecting in the wrong way.

It might also be a problem of memory
maybe namd is filling the file system. To be honest there are many others possible explanations.


From: Ivan Gregoretti <>
Sent: 07 March 2014 14:52
To: Cosseddu, Salvatore
Cc: list
Subject: Re: namd-l: Monitoring progress of an ongoing molecular dynamics simulation

Hello Salvatore,

I should have anticipated that response. Indeed, looking at the tail
of the .log file is what I've been doing but the system is buffering
the output in memory instead of writing to to the file.

Perhaps this is an anomaly and the simulation crashed even though all
processors continue working at full speed.

Any thoughts?


Ivan Gregoretti, PhD

On Fri, Mar 7, 2014 at 9:21 AM, Cosseddu, Salvatore
<> wrote:
> Dear Ivan,
> When you submit a calculation you usually use something like
> $ namd2 file.conf > file.log
> You you want to monitor the simulation you can just use
> $ tail -f file.log
> or
> $ less file.log
> and then press "F". If you want your output to be written more often you can change output frequency parameters such as outputEnergies.
> Regards
> Salvatore
> ________________________________________
> From: <> on behalf of Ivan Gregoretti <>
> Sent: 07 March 2014 14:08
> To: list
> Subject: namd-l: Monitoring progress of an ongoing molecular dynamics simulation
> Hello everybody,
> Could you share the way you monitor progress of an ongoing MD
> simulation? ie What simulation step, roughly?
> We need to monitor progress using command line tools, not GUI. It
> would be trivial with unix tools if the output weren't binary.
> I guess that a solution might involve VMD in text mode but all
> suggestions are welcome.
> Thank you,
> Ivan
> Ivan Gregoretti, PhD
> Bioinformatics

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