[gmx-users] ffoplsaa and sigma/epsilon values

[Dallas Warren]

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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