On Fri, Oct 25, 2013 at 11:44 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> 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 mmpbsa_energy.nab (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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 25 2013 - 09:00:06 PDT
