[gmx-users] ffoplsaa and sigma/epsilon values

Derrick Guang Yuh Lee k24dgyl at mun.ca
Wed Aug 11 16:20:04 CEST 2004

dear dr. warren

from what i have looked at on the gromacs search engine, it appears i can
calculate appropriate sigma/epsilon values for the ffoplsaa forcefield
additions by using the c6 and c12 values and rearranging equation 5.1 (p90
- g3.1.1 manual). if this is correct, than would it be possible to
calculate the sigma/epsilon values by using the ffgmx's c6/c12 values?
many thanks for the help.


 - derrick

 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca / derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
                                                              - bruce lee

On Wed, 11 Aug 2004, Dallas Warren wrote:

> Derrick,
> >i am right now attempting to edit the ffolpsaa forcefields non-bonded
> >parameters to add in a new molecule, specifically a lipid. i am running
> >gromacs v.3.1.4 and have looked through the manual to find out ways to
> >calculate  values, to of which i have yet to find something solid. i have
> >come close w/ section 5.3.3, but it has yet to answer all my questions. if
> >something could give me some insight, it would be much appreciated. thanks
> >in advance.
> There are some discussions on the list on this, I am pretty sure there
> should be a couple of emails that explicitly state the steps you need to
> follow to perform the fit.  Basically you need to iterate the non-bonding
> parameters to fit vapour pressure and density.
> There is a feature in mdrun (the -j switch) which you can use to speed up
> the process.
> Catch ya,
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
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