[AMBER-Developers] [Fwd: Re: [AMBER] NPT equilibration failed]

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 18 Aug 2015 12:13:06 -0400

-------- 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?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Tue Aug 18 2015 - 09:30:03 PDT
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