That makes sense. Thanks for the info.
Soonmin
On Tue, Jul 30, 2013 at 11:26 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Jul 30, 2013 at 9:14 AM, Soonmin Jang <bioaction.gmail.com> wrote:
>
> > Dear amber users,
> > In amber11 user manual, I see sander option "-radii" (page 21) but I am
> not
> > able to find any explanation on it. Just curious.
> >
>
> My guess is that it is a historical flag, perhaps at one point allowing
> people to input implicit solvent radii for GB/PB simulations. Since Amber
> 7 (ca. 2002, I think), the topology file itself has contained the implicit
> solvent radii (look for RADII in any prmtop), so this flag was likely
> unnecessary.
>
> It does not appear to be used anywhere. Not a single test in the test
> suite uses it, nor does the file appear to ever be opened.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Aug 06 2013 - 06:00:03 PDT
