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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>> AMBER-Developers.ambermd.org
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>>
> _______________________________________________
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--
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 - 13:00:30 PDT
