If you are using long range periodic electrostatics like PME, etc., you
need to have a neutral system to avoid getting infinite energies, hence
you need to maintain a neutral system by changing the number of
counterions. It's not clear to me what this means for your energies.
And if you're comparing the absolute energies you compute with MD for
the two systems, you probably should be aware that these values
typically have very large variances compared to any difference in
energy, so the sort of comparison you're looking for may be difficult.
Plus binding is really determined by the binding free energy, which is
somewhat more difficult to compute than simply the enthalpy of the
system.<br>
<br>
Someone else may be better able to comment on how to do what you're trying to do, as I'm not too sure.<br>
<br>
Best wishes,<br>
David Mobley<br><br><div><span class="gmail_quote">On 1/4/06, <b class="gmail_sendername">Mikko Hellgren</b> <<a href="mailto:Mikko.Hellgren@mbb.ki.se">Mikko.Hellgren@mbb.ki.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Gromacs Users!<br><br>I am doing simulations on a small peptide and looking at the binding<br>of zinc to cys. When I change the protonation of the cys (0 to -1),<br>should I counterbalance this charge with one less Cl- atom to get a
<br>neutral system, and if so why? If I compare energies between different<br>protonation states, how should I handle this change in the system<br>(with a different amount of Cl-)?<br><br>Many thanks in advance<br>Mikko Hellgren, Graduate Student at Karolinska Institutet in Sweden
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