From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Fri Jul 12 2013 - 12:33:48 CDT
nice attitude,
On Fri, Jul 12, 2013 at 12:48 PM, P.-L. Chau <pc104_at_pasteur.fr> wrote:
> > 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
> irrelevant.
>
> 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.
> >
> > http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html#namdtut
>
> And I strongly suggest that you read this:
>
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node75.html
>
> to understand my question before answering.
>
> Thank you.
>
> P-L Chau
>
> email: pc104_at_pasteur.fr
> Bioinformatique Structurale
> CNRS URA 2185
> Institut Pasteur
> 75724 Paris
> France
>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:27 CST