Re: [AMBER] ionic strength conversion between and PBSA

From: Jason Swails <>
Date: Fri, 25 Oct 2013 11:59:31 -0400

On Fri, Oct 25, 2013 at 11:44 AM, Vlad Cojocaru <> wrote:

> Yes, you are right.. when using sander it is conerted to 100 ...
> However, another strange thing I noticed is: when using mmpbsa_py_energy
> if I change the 0.1 value in _MMPBSA_pb.mdin to 100 ... In the mdout it
> appears 100000 ...
> So, it looks like even if in the _MMPBSA_pb.mdin the value is in M, the
> calculation is still done in mM .... It does the right thing after all
> but its quite hard to follow ...
> Well, I guess looking at the mmpsba_py_energy code should help ...

Oh yea... The unit conversion is done in (look at line
387), so it is still correct. I agree this is confusing -- I'll change it
in future versions to be more consistent.

Thanks for the report,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Oct 25 2013 - 09:00:06 PDT
Custom Search