[gmx-users] ffgmx: CH2-CH2 Dihedral

[Dallas Warren]

I was just wondering if someone here knows the reason for the value used 
for the CH2-CH2 dihedral in the GROMACS force field?

I have been doing some simulations containing bile salts, which have a 
short hydrocarbon chain attached to essentially cholesterol.  The chain was 
too straight, so I started to look into why this would be the case.  A 
simulation of 100 decane molecules showed chains that are very straight 
with only one, may be two gauche confirmations per chain.  Something isn't 
looking right here ;-)

So, then looked for a paper on the energies of a CH2-CH2 dihedral, pulled 
Allinger et al. J. Chem. Phys., 106(12) (1997) which is "The torsional 
conformations of butane: definitive energetics from ab initio 
methods".  The difference in energy between the anti and gauche 
conformations is 0.62 kcal/mol.  I performed an energy minimisation of 
butane in the anti and gauche confirmations and found that the energy 
difference using the GROMACS forcefield is 1.58 kcal/mol!  The energy for 
the dihedral is over twice of what it really should be, no wonder the 
chains are straight!

How was the value decided on?  It just seems to me that is a huge 
difference, even if the force field isn't meant for hydrocarbons, 
proteins/amino acids still contain chains of CH2-CH2 and those sections are 
going to be too rigid.

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 9076
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