AMBER Archive (2009)

Subject: [AMBER] general query: implicit solvation

From: Jio M (jiomm_at_yahoo.com)
Date: Tue Sep 08 2009 - 04:28:49 CDT

Dear Amber users

I have general query (may be silly)

 we do simulations in implicit solvents especially for protiens or
macromolecules which  have many atoms inside and outside the dense
structure..but if we compare it with explicit solvent only external
atoms  get interacted with solvent atoms (if solvent is not
accesible to inside atoms of the dense core)

my query is when we consider implicit solvation all the atoms will be
considered in implicit solvent (whether they are inside or outside)..
so is it not that we are "Over-expressing" the interactions because as
a rule only outside atoms should be considered

or else the interactions are already designed in implicit that only outside atoms are considered.....

thanks and regards

Jiomm

      
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