[gmx-users] LIE energy calculation!

Mikko Hellgren Mikko.Hellgren at ki.se
Thu Sep 7 11:31:39 CEST 2006

Hi Dear users, I have started to do calculations of the binding between
a protein and different ligands. I have read articles on the LIE method
and one tutorial. But still I have some quite general questions. I am
using Cut-off and NVT ensamble.

1. When I run my ligands in a water solution without the protein, should
I add counterions (Cl and Na) at physiological concentrations (about
10mM to 100mM) or make the system neutral with  one or two ions or can I
ignore any ions the simulation. 

2. Should I put any restraints on the ligand in the simulation without
the protein?

3. When I run my ligand bound to the protein. Should I put restraints
(c-alpha, all atoms) on both protein and ligand or only protein or
ligand or neither of them? My initial thought would be to put restraint
on c-alpha of the protein and let the rest of the system be "free".

One cannot avoid making mistakes if one tries to produce a set of words,
or of mathematical formulae, to describe nature. Nature is more
complicated than language or mathematics. Nevertheless, one must do
one's best to produce a set of symbols which are not to discordant with
the facts.
J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949
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