[gmx-users] NaCl

Mark Abraham mark.abraham at anu.edu.au
Mon Aug 16 22:43:48 CEST 2010

----- Original Message -----
From: nishap.patel at utoronto.ca
Date: Tuesday, August 17, 2010 3:56
Subject: [gmx-users] NaCl
To: gmx-users at 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


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