No objections. I think it's the right thing to do.
-Dan
On Tue, Aug 18, 2015 at 10:13 AM, 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 18 2015 - 09:30:05 PDT
