Re: [AMBER-Developers] Two fixes for mdout_analyzer.py

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Fri, 2 Jul 2021 11:11:57 -0400

Hey,

I just tried it, and it seems like a really nice addition to the Amber
toolkit, thanks Jason!

I can also confirm the problems, and the fixes. I also had to change
instances of show() to draw() here. Notice that there are other instances
of show() that need to be changed for other plots to work.

Thanks!

--
Gustavo Seabra.
On Thu, Jul 1, 2021 at 9:49 PM Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jul 1, 2021 at 12:10 AM Shiji Zhao <shijiz.uci.edu> wrote:
>
> > Dear Amber developers,
> >
> > I thought the original email failed to be sent to the maillist. Did you
> all
> > receive the same content three times? That's a little awkward...
> >
> > Dr. Case and Dr. Swails, sorry that I copied the original line 73 of
> > mdoutanalyzer/mdout.py to the previous email.What I mean is change it to:
> >
> > self.num_terms = int(self.num_steps / self.properties['ntpr']) + 1
> >
> > The reason is that the result of self.num_steps / self.properties['ntpr']
> > may
> > not be an integer, so that self.num_terms will be saved as a floating
> > number. Consequently, a TypeError will be thrown when a float number is
> > used to indicate the size of a numpy array.
> >
>
> Yes, this makes sense.  This is actually one of those Python 2 -> 3 issues
> where num_steps and ntpr were integers, so this would default to integer
> division in Python 2.  But my total number of steps was always set to a
> multiple of ntpr so it also makes sense that I'd never see this issue.
>
> >
> > Regarding the questions of Dr. Swail, I actually use it after every MD
> run
> > to check energy etc.
>
>
> Woah! An actual user!  Maybe we'll even hook Gustavo and Carlos ;).  FWIW,
> cpptraj can also parse mdout files also.
>
> If enough people find it useful and the occasional bug is easy enough to
> squash there's probably not much harm in keeping it in.
>
> I'll commit your int-casting fix here (not sure about the draw() vs. show()
> change -- I'd be wary of changing that given that show() had always worked
> for me).
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
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Received on Fri Jul 02 2021 - 08:30:02 PDT