Re: [AMBER] positive free energy

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 20 Aug 2014 17:36:44 -0400

On Wed, Aug 20, 2014 at 4:29 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:

> In my experience inp=2 gives far better affinities than inp=1 for
> protein-nucleic acids . As long as non-linear PB is used and sasopt=2.
> Therefore I disagree with changing the default to inp=1. In fact I would
> argue MMPBSA should not run with any defaults as users need to understand
> every single parameter.
>

‚ÄčThank you for the feedback. Obviously, bad experiences with inp=2 are‚Äč
over-expressed here, so it's good to hear the other side as well.

I think eliminating the default for inp is probably the best way to go
here. And while I agree users should know all of the relevant parameters,
it's too much of a change to rip out all of the defaults, in my opinion. I
think we've learned that silently changing them is a bad thing, so in cases
where no clear "best practice" or "most common" choice exists, that value
should be specified explicitly.

Thanks,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 20 2014 - 15:00:03 PDT
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