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 Jul 30 2013 - 20:30:03 PDT
