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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Received on Mon Sep 14 2009 - 13:33:48 PDT
