----- Original Message ----- From: nishap.pa...@utoronto.ca Date: Tuesday, August 17, 2010 3:56 Subject: [gmx-users] NaCl To: gmx-users@gromacs.org
> Hello, > > I want to simulate a simple NaCl ion in Well, technically not an ion. I reckon that even given Moore's Law will continue to hold, it will be infeasible for at least the next thousand years for you to simulate a large enough water box that the dissociation equilibrium of NaCl will actually have a single NaCl molecule present. :-) Thus even if you succeed in finding reasonable parameters, I can't see how your simulation could mean anything. > water. I know the method using genion which adds individual Na+ > and Cl- ion, but I wish to simulate Na-Cl connected rather than > free ions floating in water. When I ran the grompp command I got > the error: > No default Bond types > So I am thinking, I need to add b0 and Kb values for NaCl? Is > that correct? Yes, but that's a non-trivial process. See http://www.gromacs.org/Documentation/How-tos/Parameterization Mark
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