Agreed.
Ever since I started working with Amber (2009), one attractive of it was the “smart defaults”, i.e., in a large number of cases the defaults were good enough so the user didn’t need to change much. This setting should probably be one of those.
Gustavo Seabra
> Em 18/08/2015, à(s) 13:13, Jason Swails <jason.swails.gmail.com> escreveu:
>
> -------- 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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Received on Tue Aug 18 2015 - 09:30:06 PDT
