Re: NAMD pressureProfile command

From: P.-L. Chau (
Date: Fri Jul 12 2013 - 11:48:30 CDT

> you are supposed to run NAMD as following
> namd2 $your-code-name.conf > $any-name.log
> in .log file pressure will be record if you used "outputPressure"
> command in configuration file. You can load and use that later by NAMD
> Plot plug-in in VMD.

This time round, I am certain that you have misunderstood my question.
The pressure I am talking about is the lateral pressure (or, more
accurately, the stress tensor) of the system, not the average pressure
which is output in the *log file. So what you said above is completely

Besides, the last time I asked you a question about generating a DCD using
"outputPressure" in the 1st pass, and then analysing it in the 2nd pass,
but you never replied. That is the key to my problem.

> I strongly suggest you to download NAMD toturial and sample files and do
> it step by step.

And I strongly suggest that you read this:

to understand my question before answering.

Thank you.

P-L Chau

Bioinformatique Structurale
Institut Pasteur
75724 Paris

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