[gmx-users] Should I keep the total charge unchanged?

Mikko Hellgren Mikko.Hellgren at mbb.ki.se
Thu Jan 5 12:11:16 CET 2006

Hi Gromacs users and David,

Thank you David for your response. Ok - I will then
keep the total system neutral. The main purpose for my study would be 
verify and explain some experimental results done by others in my 
group -
the exp results are from a small peptide with different amount of cys
residues and zn atoms in vitro. I have access to bond distance to zn,
number of bonds per residue to zn and the binding energy. So I had a 
guess that I could get some results by checking different protonation 
the cys residues. Then the question comes on how to interpret the
simulations - free energy calculations seems to be tricky. Perhaps I 
look at the average energy (Coulomb + LJ) during the simulation between
the residues of interest and the zn atom. And also look at the bond
distance and some structural changes to the peptide of interest. Would 
nice to get some more response on this approach, is it ok or should 
you prefer some other approach.


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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