Re: [AMBER] How do I know if QM is working in sander.MPI?

From: Brian Radak <>
Date: Thu, 21 Nov 2013 10:07:23 -0500

The only scenario I have any disdain for is "unexpected behavior" with
unhelpful output and/or error message. Now, the lazy user part of me would
want to include as unexpected behavior situations in which I have made a
stupid input and AMBER simply doesn't do "what I intended it to do,"
although it very clearly does "what I told it to do," which is how I would
classify the current situation.

To me, this is very clearly a user error, not an AMBER error. As long as
one is not particularly put off by "extra" warnings that are meant to be
ignored, then option 1 seems to put appropriate responsibility on the user
while still giving a helpful message in cases where the result is not what
was desired.


On Thu, Nov 21, 2013 at 9:53 AM, Jason Swails <>wrote:

> On Thu, 2013-11-21 at 09:00 -0500, Brian Radak wrote:
> > I always did find that to be the most frustrating of mistakes...
> >
> > Would it be possible to add a warning if a qmmm namelist is present but
> > ignored (*i.e.* ifqnt = 0)?
> If ifqnt is explicitly set to 0 in the input file, I don't think any
> warning should be issued---it is quite easy to imagine use cases when a
> user would want to disable QM/MM and _not_ delete their entire QM/MM
> namelist.
> It's pretty easy to add a warning if ifqnt is not set in &cntrl but
> &qmmm is present. Perhaps this is not going far enough, though. The
> available options for when &qmmm exists but ifqnt is not set are:
> 1) Just print a warning to the mdout but carry on with no change to the
> existing default behavior.
> 2) Quit with an error, forcing users to either set ifqnt=0 or delete the
> &qmmm namelist to disable QM/MM.
> 3) Change the default behavior so that the default value of ifqnt is 1
> if &qmmm is present and 0 otherwise.
> Personally I think (2) is the best option, since it obeys the principle
> of least astonishment in my opinion and doesn't risk a guess where
> ambiguity exists.
> I've implemented (1) already, but it's trivial to change it to either 2
> or 3.
> Thoughts?
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

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Received on Thu Nov 21 2013 - 07:30:02 PST
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