AMBER Archive (2009)

Subject: [AMBER] question about pair wise per-residue energy decomposition; idecomp=3

Date: Wed Mar 25 2009 - 04:48:29 CDT

Dear all,

I'm interested in the energy decomposition with the pairwise per-residue
manner. From the AMBER mannual, I found the SANDER in AMBER can do this
job if we set idecomp=3 or 4. If we set GBSA=2, the Esurf (nonpolar
solvation energy) is also decomposited into pairwise form.

My question is how the Esurf can be decomposed into pairwise per-residue
form since this term is not a real pairwise energy. Could anyone tell
me the algorithm or the relevent papers that discuss about it.

Thanks in advance,


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