On Tue, Sep 13, 2016 at 12:53 AM, Irina Ivanova <irinaanatolieva.abv.bg>
wrote:
>
>
>
> Dear Amber users,
>
>
>
>
>
> I want to ask how residue decomposition in MMPBSA.py is perfromed? Are
> terms computed for individual atoms and then all atoms in a residue summed?
This is the general idea, yes.
> Why with inp=2 (default value) non-polar solvation term is always zero?
I presume because decomposition has not been implemented for per-residue
decomposition with that model.
> What is the practical difference between
> idecomp = 1 and
> idecomp = 2?
>
This is listed in the manual. If I recall correctly, the 1-4 nonbonded
terms are added either to electrostatic component or the dihedral component
of the energy terms.
HTH,
Jason
--
Jason M. Swails
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Received on Tue Sep 13 2016 - 05:30:03 PDT
