[gmx-users] octane

Erik Lindahl lindahl at stanford.edu
Tue Mar 19 17:58:52 CET 2002

David van der Spoel wrote:
> On Tue, 19 Mar 2002, Anton Feenstra wrote:
>>I'm wondering whether octane would fall in the 'small hydrocarbon'
>>regime, where the standard GROMOS97 forcefield still holds, or
>>whether I could better use Erik Lindahl's ffG43a2x 'extended' version
>>for long hydrocarbons... Any opinions on this?

Octane is probably halfway between 'long hydrocarbons' and normal 
ones... Jakob (who did the parameterization) followed a suggestion by 
Eric Jacobsen: First parameterize the 'long' CH3 parameter to get the
correct heat of vaporization & density for pentadecane, and then adjust 
the corresponding CH2 parameters to get good trends over smaller 
hydrocarbon lengths.

I think it should be ok, but we never used the parameters for anything 
but lipids.... If you are checking heat of vaporizations the 
experimental value for at least pentadecane changed significantly in the 
latter versions of CRC, so make sure you compare to updated values.



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