This is already a problem at times - we just need to be better about
warning people away from doing that, maybe with big(ger) warnings at the
top of the inputs.
I just had a student reuse a test with ntwx=2 for some very long md.
Disastrous!
On Aug 18, 2015 3:50 PM, "Adrian Roitberg" <roitberg.ufl.edu> wrote:
> I agree.
>
> But then the test cases will have a fixed ig ? I am all for it, but....
>
> I am very afraid of people lifting the mdins from the test cases and
> forgetting to change ig...
>
> I guess it is a case of foolproofing creating more fools ?
>
> adrian
>
>
> On 8/18/15 3:48 PM, Hai Nguyen wrote:
> > +1 for default ig=-1. I myself got periodic result a while ago and need
> to
> > rerun my sims.
> >
> > Hai
> >
> > On Tue, Aug 18, 2015 at 12:13 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> >> -------- Forwarded Message --------
> >>> From: Adrian Roitberg <roitberg.ufl.edu>
> >>> Reply-to: AMBER Mailing List <amber.ambermd.org>
> >>> To: AMBER Mailing List <amber.ambermd.org>
> >>> Subject: Re: [AMBER] NPT equilibration failed
> >>> Date: Tue, 18 Aug 2015 09:02:38 -0400
> >>> Also PLEASE PLEASE PLEASE add ig=-1 to your langevin thermostat inputs!
> >>> Oterwise you can see unphysical behaviors. Please look at the manual
> for
> >>> the origin of this requirement.
> >> I think we should change the default value of ig to -1. Keeping the
> >> default value is almost always the wrong thing to do, but it is not
> >> obviously wrong, which makes it a dangerous default in my opinion. I
> >> think that ig=-1 is almost always a better default for ig and never a
> >> worse one.
> >>
> >> The main issue with changing the default is going to be updating the
> >> tests to specify an explicit seed where the current default is relied
> >> upon for reproducibility. But that is easily worth fixing the default.
> >>
> >> Does anybody have particularly strong objections to this?
> >>
> >> Thanks,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >>
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> --
> Dr. Adrian E. Roitberg
> Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Tue Aug 18 2015 - 13:30:03 PDT
